6zsd - Revision history

OCA at 14:51, 6 March 2024

OCA — Wed, 06 Mar 2024 14:51:38 GMT

←Older revision		Revision as of 14:51, 6 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/RT17_HUMAN RT17_HUMAN]		[https://www.uniprot.org/uniprot/RT17_HUMAN RT17_HUMAN]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 A resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes.
-
-	Structural basis of mitochondrial translation.,Aibara S, Singh V, Modelska A, Amunts A Elife. 2020 Aug 19;9. pii: 58362. doi: 10.7554/eLife.58362. PMID:32812867<ref>PMID:32812867</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6zsd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:54, 15 November 2023

OCA — Wed, 15 Nov 2023 10:54:09 GMT

←Older revision		Revision as of 10:54, 15 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6zsd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZSD FirstGlance]. <br>		<table><tr><td colspan='2'>[[6zsd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZSD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</scene>, <scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene>, <scene name='pdbligand=Y5P:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,4-DIHYDROPYRIMIDINE'>Y5P</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">Electron Microscopy, [[Resolution\|Resolution]] 3.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</scene>, <scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene>, <scene name='pdbligand=Y5P:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,4-DIHYDROPYRIMIDINE'>Y5P</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [https://pdbe.org/6zsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [https://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd 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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [https://pdbe.org/6zsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [https://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:44, 11 January 2023

OCA — Wed, 11 Jan 2023 07:44:37 GMT

←Older revision		Revision as of 07:44, 11 January 2023
Line 1:		Line 1:

-	====	+	==Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA==
-	<StructureSection load='6zsd' size='340' side='right'caption='[[6zsd]]' scene=''>	+	<StructureSection load='6zsd' size='340' side='right'caption='[[6zsd]], [[Resolution\|resolution]] 3.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zsd]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZSD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZSD FirstGlance]. <br>
-	</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [https://pdbe.org/6zsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [https://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=004:(2S)-AMINO(PHENYL)ETHANOIC+ACID'>004</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <scene name='pdbligand=DOL:5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE'>DOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MHT:(3S)-3-(METHYLSULFANYL)-1-AZABICYCLO[2.2.2]OCTANE'>MHT</scene>, <scene name='pdbligand=MHU:4-N,N-(DIMETHYLAMINO)-L-PHENYLALANINE'>MHU</scene>, <scene name='pdbligand=MHV:4-OXO-L-PIPECOLIC+ACID'>MHV</scene>, <scene name='pdbligand=MHW:3-HYDROXYPICOLINIC+ACID'>MHW</scene>, <scene name='pdbligand=P5P:PURINE+RIBOSIDE-5-MONOPHOSPHATE'>P5P</scene>, <scene name='pdbligand=Y5P:1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1,4-DIHYDROPYRIMIDINE'>Y5P</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [https://pdbe.org/6zsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [https://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RT17_HUMAN RT17_HUMAN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Translation of mitochondrial messenger RNA (mt-mRNA) is performed by distinct mitoribosomes comprising at least 36 mitochondria-specific proteins. How these mitoribosomal proteins assist in the binding of mt-mRNA and to what extent they are involved in the translocation of transfer RNA (mt-tRNA) is unclear. To visualize the process of translation in human mitochondria, we report ~3.0 A resolution structure of the human mitoribosome, including the L7/L12 stalk, and eight structures of its functional complexes with mt-mRNA, mt-tRNAs, recycling factor and additional trans factors. The study reveals a transacting protein module LRPPRC-SLIRP that delivers mt-mRNA to the mitoribosomal small subunit through a dedicated platform formed by the mitochondria-specific protein mS39. Mitoribosomal proteins of the large subunit mL40, mL48, and mL64 coordinate translocation of mt-tRNA. The comparison between those structures shows dynamic interactions between the mitoribosome and its ligands, suggesting a sequential mechanism of conformational changes.
		+
		+	Structural basis of mitochondrial translation.,Aibara S, Singh V, Modelska A, Amunts A Elife. 2020 Aug 19;9. pii: 58362. doi: 10.7554/eLife.58362. PMID:32812867<ref>PMID:32812867</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zsd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Aibara S]]
		+	[[Category: Amunts A]]
		+	[[Category: Modelska A]]
		+	[[Category: Singh V]]

OCA at 06:51, 24 March 2021

OCA — Wed, 24 Mar 2021 06:51:16 GMT

←Older revision		Revision as of 06:51, 24 March 2021
Line 3:		Line 3:
	<StructureSection load='6zsd' size='340' side='right'caption='[[6zsd]]' scene=''>		<StructureSection load='6zsd' size='340' side='right'caption='[[6zsd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [~~http~~://pdbe.org/6zsd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>	+	</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [https://pdbe.org/6zsd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [https://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 09:54, 16 September 2020

OCA — Wed, 16 Sep 2020 09:54:16 GMT

←Older revision		Revision as of 09:54, 16 September 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zsd ~~is ON HOLD~~	+	====
-		+	<StructureSection load='6zsd' size='340' side='right'caption='[[6zsd]]' scene=''>
-	~~Authors~~: ~~Aibara, S~~.~~, Singh, V~~.~~, Modelska, A~~.~~, Amunts, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Human mitochondrial ribosome in complex with mRNA~~, ~~P-site tRNA and E-site tRNA~~	+	</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=6zsd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zsd OCA], [http://pdbe.org/6zsd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zsd RCSB], [http://www.ebi.ac.uk/pdbsum/6zsd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zsd ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[~~[Category~~: ~~Amunts, A~~]]	+	__TOC__
-	[~~[Category~~: ~~Modelska~~, A]]	+	</StructureSection>
-	[[Category: ~~Aibara, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Singh, V~~]]	+	[[Category: Z-disk]]

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

OCA — Wed, 22 Jul 2020 08:20:14 GMT

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

←Older revision

Revision as of 08:20, 22 July 2020

OCA: New page: '''Unreleased structure''' The entry 6zsd is ON HOLD Authors: Aibara, S., Singh, V., Modelska, A., Amunts, A. Description: Human mitochondrial ribosome in complex with mRNA, P-site tRN...

OCA — Wed, 22 Jul 2020 08:20:13 GMT

New page: '''Unreleased structure''' The entry 6zsd is ON HOLD Authors: Aibara, S., Singh, V., Modelska, A., Amunts, A. Description: Human mitochondrial ribosome in complex with mRNA, P-site tRN...

New page

'''Unreleased structure'''

The entry 6zsd is ON HOLD

Authors: Aibara, S., Singh, V., Modelska, A., Amunts, A.

Description: Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA
[[Category: Unreleased Structures]]
[[Category: Amunts, A]]
[[Category: Modelska, A]]
[[Category: Aibara, S]]
[[Category: Singh, V]]