6orb - Revision history

OCA at 14:53, 13 March 2024

2024-03-13T14:53:00Z

← Older revision		Revision as of 14:53, 13 March 2024
Line 3:		Line 3:
	<SX load='6orb' size='340' side='right' viewer='molstar' caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>		<SX load='6orb' size='340' side='right' viewer='molstar' caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6ORB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ORB FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~mdn1~~, ~~SPCC737.08 (~~[~~http://www.ncbi~~.~~nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=4896 CBS 356])~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 7.7Å</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [~~http~~://pdbe.org/6orb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6orb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb 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=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [https://pdbe.org/6orb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [https://www.ebi.ac.uk/pdbsum/6orb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/MDN1_SCHPO MDN1_SCHPO]] Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits. Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre-60S particles from the nucleolus and then driving late pre-60S particles from the nucleus.[UniProtKB:Q12019]		[https://www.uniprot.org/uniprot/MDN1_SCHPO MDN1_SCHPO] Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits. Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre-60S particles from the nucleolus and then driving late pre-60S particles from the nucleus.[UniProtKB:Q12019]
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size ( approximately 5,000 amino acid [aa]) and its limited homology to other well-studied proteins have restricted our understanding of its remodeling function. Here, we present structures for S. pombe Mdn1 in the presence of AMPPNP at up to approximately 4 A or ATP plus Rbin-1, a chemical inhibitor, at approximately 8 A resolution. These data reveal that Mdn1's MIDAS domain is tethered to its ring-shaped AAA domain through an approximately 20 nm long structured linker and a flexible approximately 500 aa Asp/Glu-rich motif. We find that the MIDAS domain, which also binds other ribosome-assembly factors, docks onto the AAA ring in a nucleotide state-specific manner. Together, our findings reveal how conformational changes in the AAA ring can be directly transmitted to the MIDAS domain and thereby drive the targeted release of assembly factors from ribosomal 60S-subunit precursors.

	Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.,Chen Z, Suzuki H, Kobayashi Y, Wang AC, DiMaio F, Kawashima SA, Walz T, Kapoor TM Cell. 2018 Oct 18;175(3):822-834.e18. doi: 10.1016/j.cell.2018.09.015. Epub 2018 , Oct 11. PMID:30318141<ref>PMID:30318141</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6orb" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</SX>		</SX>
	~~[[Category: Cbs 356]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen, Z]]		[[Category: Schizosaccharomyces pombe]]
	[[Category: DiMaio, F]]		[[Category: Chen Z]]
	[[Category: Kapoor~~, T M~~]]		[[Category: DiMaio F]]
	[[Category: Suzuki, H]]		[[Category: Kapoor TM]]
	[[Category: Walz, T]]		[[Category: Suzuki H]]
	[[Category: Wang~~, A C]]~~		[[Category: Walz T]]
	~~[[Category: Aaa protein]]~~		[[Category: Wang AC]]
	~~[[Category: Mechanochemical enzyme]]~~
	~~[[Category: Motor protein]]~~
	~~[[Category: Ribosome assembly factor]]~~
	~~[[Category: Ribosome biogenesis~~]]

OCA at 04:08, 11 April 2020

2020-04-11T04:08:58Z

← Older revision		Revision as of 04:08, 11 April 2020
Line 3:		Line 3:
	<SX load='6orb' size='340' side='right' viewer='molstar' caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>		<SX load='6orb' size='340' side='right' viewer='molstar' caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ORB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ORB FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdn1, SPCC737.08 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdn1, SPCC737.08 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [http://pdbe.org/6orb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [http://www.ebi.ac.uk/pdbsum/6orb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [http://pdbe.org/6orb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [http://www.ebi.ac.uk/pdbsum/6orb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 23:16, 6 March 2020

2020-03-06T23:16:40Z

← Older revision		Revision as of 23:16, 6 March 2020
Line 1:		Line 1:

	==Full-length S. pombe Mdn1 in the presence of ATP and Rbin-1==		==Full-length S. pombe Mdn1 in the presence of ATP and Rbin-1==
	<~~StructureSection~~ load='6orb' size='340' side='right'caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>		<SX load='6orb' size='340' side='right' viewer='molstar' caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORB FirstGlance]. <br>
Line 21:		Line 21:
	<references/>		<references/>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	[[Category: Cbs 356]]		[[Category: Cbs 356]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 12:11, 18 December 2019

2019-12-18T12:11:00Z

← Older revision		Revision as of 12:11, 18 December 2019
Line 3:		Line 3:
	<StructureSection load='6orb' size='340' side='right'caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>		<StructureSection load='6orb' size='340' side='right'caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORB FirstGlance]. <br>
	</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=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [http://pdbe.org/6orb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [http://www.ebi.ac.uk/pdbsum/6orb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mdn1, SPCC737.08 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [http://pdbe.org/6orb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [http://www.ebi.ac.uk/pdbsum/6orb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Cbs 356]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Chen, Z]]		[[Category: Chen, Z]]

OCA at 05:58, 29 May 2019

2019-05-29T05:58:43Z

← Older revision		Revision as of 05:58, 29 May 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The~~ entry 6orb is ~~ON HOLD~~		==Full-length S. pombe Mdn1 in the presence of ATP and Rbin-1==
			<StructureSection load='6orb' size='340' side='right'caption='[[6orb]], [[Resolution\|resolution]] 7.70Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6orb]] is a 1 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6ees 6ees]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ORB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ORB FirstGlance]. <br>
			</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=6orb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6orb OCA], [http://pdbe.org/6orb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6orb RCSB], [http://www.ebi.ac.uk/pdbsum/6orb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6orb ProSAT]</span></td></tr>
			</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/MDN1_SCHPO MDN1_SCHPO]] Nuclear chaperone required for maturation and nuclear export of pre-60S ribosome subunits. Functions at successive maturation steps to remove ribosomal factors at critical transition points, first driving the exit of early pre-60S particles from the nucleolus and then driving late pre-60S particles from the nucleus.[UniProtKB:Q12019]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Mdn1 is an essential AAA (ATPase associated with various activities) protein that removes assembly factors from distinct precursors of the ribosomal 60S subunit. However, Mdn1's large size ( approximately 5,000 amino acid [aa]) and its limited homology to other well-studied proteins have restricted our understanding of its remodeling function. Here, we present structures for S. pombe Mdn1 in the presence of AMPPNP at up to approximately 4 A or ATP plus Rbin-1, a chemical inhibitor, at approximately 8 A resolution. These data reveal that Mdn1's MIDAS domain is tethered to its ring-shaped AAA domain through an approximately 20 nm long structured linker and a flexible approximately 500 aa Asp/Glu-rich motif. We find that the MIDAS domain, which also binds other ribosome-assembly factors, docks onto the AAA ring in a nucleotide state-specific manner. Together, our findings reveal how conformational changes in the AAA ring can be directly transmitted to the MIDAS domain and thereby drive the targeted release of assembly factors from ribosomal 60S-subunit precursors.

	~~Authors:~~ Chen, Z., Suzuki, H., Wang~~, A.C.~~, DiMaio, F., Walz, T., Kapoor, ~~T.M~~.		Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis.,Chen Z, Suzuki H, Kobayashi Y, Wang AC, DiMaio F, Kawashima SA, Walz T, Kapoor TM Cell. 2018 Oct 18;175(3):822-834.e18. doi: 10.1016/j.cell.2018.09.015. Epub 2018 , Oct 11. PMID:30318141<ref>PMID:30318141</ref>

	~~Description: Full-length~~ S. ~~pombe Mdn1 in the presence~~ of ~~ATP and Rbin~~-1		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[Category: Unreleased Structures]]~~		</div>
	~~[[Category: Walz, T]]~~		<div class="pdbe-citations 6orb" style="background-color:#fffaf0;"></div>
	~~[[Category: Dimaio, F]]~~		== References ==
	[[Category: ~~Kapoor, T.M~~]]		<references/>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
	[[Category: Chen, Z]]		[[Category: Chen, Z]]
			[[Category: DiMaio, F]]
			[[Category: Kapoor, T M]]
	[[Category: Suzuki, H]]		[[Category: Suzuki, H]]
	[[Category: Wang, A.C]]		[[Category: Walz, T]]
			[[Category: Wang, A C]]
			[[Category: Aaa protein]]
			[[Category: Mechanochemical enzyme]]
			[[Category: Motor protein]]
			[[Category: Ribosome assembly factor]]
			[[Category: Ribosome biogenesis]]

OCA: Protected "6orb" [edit=sysop:move=sysop]

2019-05-10T08:02:09Z

Protected "6orb" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:02, 10 May 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6orb is ON HOLD Authors: Chen, Z., Suzuki, H., Wang, A.C., DiMaio, F., Walz, T., Kapoor, T.M. Description: Full-length S. pombe Mdn1 in the presenc...

2019-05-10T08:02:06Z

New page: '''Unreleased structure''' The entry 6orb is ON HOLD Authors: Chen, Z., Suzuki, H., Wang, A.C., DiMaio, F., Walz, T., Kapoor, T.M. Description: Full-length S. pombe Mdn1 in the presenc...

New page

'''Unreleased structure'''

The entry 6orb is ON HOLD

Authors: Chen, Z., Suzuki, H., Wang, A.C., DiMaio, F., Walz, T., Kapoor, T.M.

Description: Full-length S. pombe Mdn1 in the presence of ATP and Rbin-1
[[Category: Unreleased Structures]]
[[Category: Walz, T]]
[[Category: Dimaio, F]]
[[Category: Kapoor, T.M]]
[[Category: Chen, Z]]
[[Category: Suzuki, H]]
[[Category: Wang, A.C]]