4kvb - Revision history

OCA at 16:05, 20 September 2023

2023-09-20T16:05:55Z

← Older revision		Revision as of 16:05, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 4.198Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [https://pdbe.org/4kvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [https://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [https://pdbe.org/4kvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [https://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:16, 7 December 2022

2022-12-07T09:16:18Z

← Older revision		Revision as of 09:16, 7 December 2022
Line 3:		Line 3:
	<StructureSection load='4kvb' size='340' side='right'caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='4kvb' size='340' side='right'caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thermus_thermophilus~~ Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvb]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	~~<tr~~ id~~='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class~~="~~sblockDat~~"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene><~~/td></tr>~~		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [https://pdbe.org/4kvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [https://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[4ji5\|4ji5]]~~</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [~~http~~://pdbe.org/4kvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[~~http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with~~ protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).		[https://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity).

			==See Also==
			*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus HB27]]
	[[Category: Jogl, G]]		[[Category: Jogl G]]
	[[Category: Murphy~~, E L]]~~		[[Category: Murphy EL]]
	~~[[Category: 30s ribosomal subunit]]~~
	~~[[Category: 50s ribosomal subunit]]~~
	~~[[Category: Ribosome]]~~
	~~[[Category: Translation~~]]

OCA at 05:27, 13 February 2020

2020-02-13T05:27:22Z

← Older revision		Revision as of 05:27, 13 February 2020
Line 1:		Line 1:
	~~{{Large structure}}~~
	==Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17==		==Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17==
	<StructureSection load='4kvb' size='340' side='right' caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='4kvb' size='340' side='right'caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVB FirstGlance]. <br>
Line 9:		Line 9:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://pdbe.org/4kvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://pdbe.org/4kvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>
	</table>		</table>
	~~{{Large structure}}~~
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/~~RS18_THET2 RS18_THET2~~]] ~~Binds as a heterodimer with protein S6 to~~ the ~~central domain~~ of the ~~16S rRNA, where it helps stabilize the platform~~ of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/~~RS19_THET2 RS19_THET2~~]] ~~Protein S19 forms~~ a ~~complex~~ with ~~S13 that binds strongly~~ to the ~~16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part~~ of the ~~body of the 30S subunit~~, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit~~. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA~~ (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).		[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Jogl, G]]		[[Category: Jogl, G]]

OCA at 09:27, 15 November 2017

2017-11-15T09:27:32Z

← Older revision		Revision as of 09:27, 15 November 2017
Line 11:		Line 11:
	{{Large structure}}		{{Large structure}}
	== Function ==		== Function ==
	~~[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity).~~ [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome ~~(By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation~~ (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/~~RS9_THET2 RS9_THET2~~]] ~~Part~~ of the ~~top of~~ the ~~head~~ of the 30S subunit~~. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA~~ (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/~~RS18_THET2 RS18_THET2~~]] ~~Binds as~~ a ~~heterodimer~~ with ~~protein S6~~ to the ~~central domain~~ of the 16S rRNA, ~~where~~ it ~~helps stabilize~~ the ~~platform~~ of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit ~~(By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA~~ (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).		[[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 17:55, 5 August 2016

2016-08-05T17:55:05Z

← Older revision		Revision as of 17:55, 5 August 2016
Line 1:		Line 1:
			{{Large structure}}
	==Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17==		==Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17==
	<StructureSection load='4kvb' size='340' side='right' caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='4kvb' size='340' side='right' caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ji5\|4ji5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ji5\|4ji5]]</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://pdbe.org/4kvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kvb ProSAT]</span></td></tr>
	</table>		</table>
			{{Large structure}}
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).		[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).

OCA at 04:37, 25 December 2014

2014-12-25T04:37:20Z

← Older revision		Revision as of 04:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVB FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ji5\|4ji5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ji5\|4ji5]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/RS6_THET2 RS6_THET2]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA (By similarity). [[http://www.uniprot.org/uniprot/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THET2 RS12_THET2]] With S4 and S5 plays an important role in translational accuracy (By similarity). Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RSHX_THET2 RSHX_THET2]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS15_THET2 RS15_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS14Z_THET2 RS14Z_THET2]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS8_THET2 RS8_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS19_THET2 RS19_THET2]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS20_THET2 RS20_THET2]] Binds directly to 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THET2 RS10_THET2]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RS5_THET2 RS5_THET2]] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Jogl, G.]]		[[Category: Jogl, G]]
	[[Category: Murphy, E L.]]		[[Category: Murphy, E L]]
	[[Category: 30s ribosomal subunit]]		[[Category: 30s ribosomal subunit]]
	[[Category: 50s ribosomal subunit]]		[[Category: 50s ribosomal subunit]]
	[[Category: Ribosome]]		[[Category: Ribosome]]
	[[Category: Translation]]		[[Category: Translation]]

OCA at 05:11, 4 June 2014

2014-06-04T05:11:44Z

← Older revision		Revision as of 05:11, 4 June 2014
Line 1:		Line 1:
	'''~~Unreleased structure~~'''		==Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17==
			<StructureSection load='4kvb' size='340' side='right' caption='[[4kvb]], [[Resolution\|resolution]] 4.20Å' scene=''>
	~~The entry~~ 4kvb is ~~ON HOLD~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[4kvb]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KVB FirstGlance]. <br>
	~~Authors~~: ~~Murphy~~, E.L., Jogl, G.		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
	~~Description~~: ~~Thermus thermophilus HB27 30S~~ ribosomal subunit ~~lacking~~ ribosomal ~~protein S17~~		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ji5\|4ji5]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kvb RCSB], [http://www.ebi.ac.uk/pdbsum/4kvb PDBsum]</span></td></tr>
			<table>
			__TOC__
			</StructureSection>
			[[Category: Thermus thermophilus]]
			[[Category: Jogl, G.]]
			[[Category: Murphy, E L.]]
			[[Category: 30s ribosomal subunit]]
			[[Category: 50s ribosomal subunit]]
			[[Category: Ribosome]]
			[[Category: Translation]]

OCA: Protected "4kvb" [edit=sysop:move=sysop]

2013-06-19T12:05:33Z

Protected "4kvb" [edit=sysop:move=sysop]

← Older revision	Revision as of 12:05, 19 June 2013
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4kvb is ON HOLD Authors: Murphy, E.L., Jogl, G. Description: Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

2013-06-19T12:05:31Z

New page: '''Unreleased structure''' The entry 4kvb is ON HOLD Authors: Murphy, E.L., Jogl, G. Description: Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17

New page

'''Unreleased structure'''

The entry 4kvb is ON HOLD

Authors: Murphy, E.L., Jogl, G.

Description: Thermus thermophilus HB27 30S ribosomal subunit lacking ribosomal protein S17