1fka: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
Line 3: Line 3:
<StructureSection load='1fka' size='340' side='right'caption='[[1fka]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
<StructureSection load='1fka' size='340' side='right'caption='[[1fka]], [[Resolution|resolution]] 3.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1fka]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The October 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribosome''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_10 10.2210/rcsb_pdb/mom_2000_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKA FirstGlance]. <br>
<table><tr><td colspan='2'>[[1fka]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. The October 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Ribosome''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_10 10.2210/rcsb_pdb/mom_2000_10]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FKA FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=WO2:OCTADECATUNGSTENYL+DIPHOSPHATE'>WO2</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]] 3.3&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=WO2:OCTADECATUNGSTENYL+DIPHOSPHATE'>WO2</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1c05|1c05]], [[1pkp|1pkp]], [[1ris|1ris]], [[1rss|1rss]], [[1an7|1an7]], [[1a32|1a32]], [[1ekc|1ekc]], [[1qkf|1qkf]]</div></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=1fka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fka OCA], [https://pdbe.org/1fka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fka RCSB], [https://www.ebi.ac.uk/pdbsum/1fka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fka 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=1fka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fka OCA], [https://pdbe.org/1fka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fka RCSB], [https://www.ebi.ac.uk/pdbsum/1fka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fka ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 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. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[https://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] 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.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[https://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] 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). [[https://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] 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. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[https://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]  
[https://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8] 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. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 21: Line 20:
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1fka ConSurf].
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1fka ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The small ribosomal subunit performs the decoding of genetic information during translation. The structure of that from Thermus thermophilus shows that the decoding center, which positions mRNA and three tRNAs, is constructed entirely of RNA. The entrance to the mRNA channel will encircle the message when a latch-like contact closes and contributes to processivity and fidelity. Extended RNA helical elements that run longitudinally through the body transmit structural changes, correlating events at the particle's far end with the cycle of mRNA translocation at the decoding region. 96% of the nucleotides were traced and the main fold of all proteins was determined. The latter are either peripheral or appear to serve as linkers. Some may assist the directionality of translocation.
Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution.,Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A Cell. 2000 Sep 1;102(5):615-23. PMID:11007480<ref>PMID:11007480</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1fka" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Ribosome|Ribosome]]
*[[Ribosome|Ribosome]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
Line 42: Line 30:
[[Category: Ribosome]]
[[Category: Ribosome]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Agmon, I]]
[[Category: Agmon I]]
[[Category: Bartels, H]]
[[Category: Bartels H]]
[[Category: Bashan, A]]
[[Category: Bashan A]]
[[Category: Franceschi, F]]
[[Category: Franceschi F]]
[[Category: Gluehmann, M]]
[[Category: Gluehmann M]]
[[Category: Harms, J]]
[[Category: Harms J]]
[[Category: Janell, D]]
[[Category: Janell D]]
[[Category: Schluenzen, F]]
[[Category: Schluenzen F]]
[[Category: Tocilj, A]]
[[Category: Tocilj A]]
[[Category: Yonath, A]]
[[Category: Yonath A]]
[[Category: Zarivach, R]]
[[Category: Zarivach R]]
[[Category: 30s ribosomal subunit]]
[[Category: Protein-rna complex]]

Revision as of 07:15, 7 February 2024

STRUCTURE OF FUNCTIONALLY ACTIVATED SMALL RIBOSOMAL SUBUNIT AT 3.3 A RESOLUTION

1fka, resolution 3.30Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=1fka&oldid=4043532"