7kq5 - Revision history

OCA at 14:57, 6 March 2024

2024-03-06T14:57:23Z

←Older revision		Revision as of 14:57, 6 March 2024
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	<StructureSection load='7kq5' size='340' side='right'caption='[[7kq5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='7kq5' size='340' side='right'caption='[[7kq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KQ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KQ5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TM_0785 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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=7kq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kq5 OCA], [https://pdbe.org/7kq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kq5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kq5 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=7kq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kq5 OCA], [https://pdbe.org/7kq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kq5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kq5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~MARIT_THEMA MARIT_THEMA~~]~~] Protease that exhibits activity toward chymotrypsin and trypsin substrates~~. ~~May have antibacterial activity.~~	+	[https://www.uniprot.org/uniprot/ENCAP_THEMA ENCAP_THEMA] Shell component of a type 1 encapsulin nanocompartment. Assembles into proteinaceous shells 23-24 nm in diameter with 2-2.5 nm thick walls. Cargo protein Flp (ferritin-like protein, may store iron) is targeted to the interior via its C-terminal extension; empty intact shells can be isolated in the absence of cargo protein (PubMed:19172747, PubMed:27224728, PubMed:32961724, PubMed:30376298, PubMed:33769792, PubMed:33953921, PubMed:34815415). Fe(2+) may be able to pass though the 5-fold and dimer channels in the protein shell (Probable).<ref>PMID:19172747</ref> <ref>PMID:27224728</ref> <ref>PMID:30376298</ref> <ref>PMID:32961724</ref> <ref>PMID:33769792</ref> <ref>PMID:33953921</ref> <ref>PMID:34815415</ref> <ref>PMID:33953921</ref> Protease that exhibits activity toward chymotrypsin and trypsin substrates (PubMed:9872409, PubMed:11210524). Probably does not have antibacterial activity (Probable).<ref>PMID:11210524</ref> <ref>PMID:9872409</ref> <ref>PMID:19172747</ref>
-	~~<div style="background~~-~~color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Protein nanocompartments are widespread~~ in ~~bacteria and archaea, but their functions are not yet well understood. Here, the cryo~~-~~EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at~~ 2.~~0 A resolution~~. ~~The high resolution of this structure shows that interactions in the E~~-~~loop domain~~ may be ~~important for~~ the ~~thermostability~~ of ~~the nanocompartment assembly. Also~~, ~~the channels at the fivefold axis~~, ~~threefold axis and dimer interface are assessed for their ability to transport iron. Finally~~, ~~an unexpected flavin ligand was identified on the exterior of the shell~~, ~~indicating that this nanocompartment may also play a direct role in iron metabolism.~~	+
-		+
-	~~Cryo-EM structure of a thermostable bacterial nanocompartment.~~,~~Wiryaman T~~, ~~Toor N IUCrJ~~. ~~2021 Apr 2;8~~(~~Pt 3~~)~~:342~~-~~350~~. ~~doi~~: ~~10.1107~~/~~S2052252521001949. eCollection, 2021 May 1.~~ PMID:~~33953921~~<ref>PMID:33953921</ref>	+
-		+
-	~~From MEDLINE®~~/PubMed~~®~~, ~~a database of the U~~.~~S. National Library of Medicine~~.<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 7kq5" style="background-color~~:~~#fffaf0;"~~></~~div~~>	+
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thema~~]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: Toor, N]]	+	[[Category: Toor N]]
-	[[Category: Wiryaman~~, T I]]~~	+	[[Category: Wiryaman TI]]
-	~~[[Category: Encapsulin]]~~	+
-	~~[[Category: Flavin-binding]]~~	+
-	~~[[Category: Hk97 fold]]~~	+
-	~~[[Category: Icosahedral]]~~	+
-	~~[[Category: Virus like particle~~]]	+

OCA at 10:25, 19 May 2021

2021-05-19T10:25:44Z

←Older revision		Revision as of 10:25, 19 May 2021
Line 10:		Line 10:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/MARIT_THEMA MARIT_THEMA]] Protease that exhibits activity toward chymotrypsin and trypsin substrates. May have antibacterial activity.		[[https://www.uniprot.org/uniprot/MARIT_THEMA MARIT_THEMA]] Protease that exhibits activity toward chymotrypsin and trypsin substrates. May have antibacterial activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at 2.0 A resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.
		+
		+	Cryo-EM structure of a thermostable bacterial nanocompartment.,Wiryaman T, Toor N IUCrJ. 2021 Apr 2;8(Pt 3):342-350. doi: 10.1107/S2052252521001949. eCollection, 2021 May 1. PMID:33953921<ref>PMID:33953921</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kq5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 09:39, 12 May 2021

2021-05-12T09:39:43Z

←Older revision		Revision as of 09:39, 12 May 2021
Line 1:		Line 1:

	==Cryo-EM structure of a thermostable encapsulin from T. maritima==		==Cryo-EM structure of a thermostable encapsulin from T. maritima==
-	<StructureSection load='7kq5' size='340' side='right'caption='[[7kq5]]' scene=''>	+	<StructureSection load='7kq5' size='340' side='right'caption='[[7kq5]], [[Resolution\|resolution]] 2.00Å' 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=7KQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KQ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KQ5 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=7kq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kq5 OCA], [https://pdbe.org/7kq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kq5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kq5 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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_0785 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=7kq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kq5 OCA], [https://pdbe.org/7kq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kq5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kq5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/MARIT_THEMA MARIT_THEMA]] Protease that exhibits activity toward chymotrypsin and trypsin substrates. May have antibacterial activity.
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Toor N]]	+	[[Category: Thema]]
-	[[Category: Wiryaman TI]]	+	[[Category: Toor, N]]
		+	[[Category: Wiryaman, T I]]
		+	[[Category: Encapsulin]]
		+	[[Category: Flavin-binding]]
		+	[[Category: Hk97 fold]]
		+	[[Category: Icosahedral]]
		+	[[Category: Virus like particle]]

OCA at 05:21, 28 April 2021

2021-04-28T05:21:52Z

←Older revision		Revision as of 05:21, 28 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kq5 ~~is ON HOLD~~	+	==Cryo-EM structure of a thermostable encapsulin from T. maritima==
-		+	<StructureSection load='7kq5' size='340' side='right'caption='[[7kq5]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KQ5 FirstGlance]. <br>
-	~~Description~~:	+	</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=7kq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kq5 OCA], [https://pdbe.org/7kq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kq5 RCSB], [https://www.ebi.ac.uk/pdbsum/7kq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kq5 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Toor N]]
		+	[[Category: Wiryaman TI]]

OCA: Protected "7kq5" [edit=sysop:move=sysop]

2020-11-25T05:32:35Z

Protected "7kq5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:32, 25 November 2020

OCA: New page: '''Unreleased structure''' The entry 7kq5 is ON HOLD Authors: Description: Category: Unreleased Structures

2020-11-25T05:32:34Z

New page: '''Unreleased structure''' The entry 7kq5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kq5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]