8dwj - Revision history

OCA at 07:46, 23 August 2023

OCA — Wed, 23 Aug 2023 07:46:24 GMT

←Older revision		Revision as of 07:46, 23 August 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8dwj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T4 Escherichia phage T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DWJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[8dwj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T4 Escherichia phage T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DWJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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]] 3.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=8dwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dwj OCA], [https://pdbe.org/8dwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dwj RCSB], [https://www.ebi.ac.uk/pdbsum/8dwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dwj 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=8dwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dwj OCA], [https://pdbe.org/8dwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dwj RCSB], [https://www.ebi.ac.uk/pdbsum/8dwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dwj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:18, 14 June 2023

OCA — Wed, 14 Jun 2023 08:18:25 GMT

←Older revision		Revision as of 08:18, 14 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8dwj is ~~ON HOLD~~	+	==Primase of mutant bacteriophage T4 primosome with single strand DNA/RNA primer hybrid in primer exiting state==
		+	<StructureSection load='8dwj' size='340' side='right'caption='[[8dwj]], [[Resolution\|resolution]] 3.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8dwj]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T4 Escherichia phage T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DWJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=8dwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dwj OCA], [https://pdbe.org/8dwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dwj RCSB], [https://www.ebi.ac.uk/pdbsum/8dwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dwj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PRIM_BPT4 PRIM_BPT4] Synthesizes short RNA primers for the lagging strand DNA replication (PubMed:2422175, PubMed:3038901, PubMed:11735390, PubMed:22869700). The primase synthesizes short RNA primers on the lagging strand that the polymerase elongates using dNTPs (PubMed:2422175, PubMed:3038901). Recognizes two trinucleotide sequences 5'-GTT-3' and 5'-GCT-3' in vitro, but uses only the first as the priming site in vivo (PubMed:2422175).[HAMAP-Rule:MF_04157]<ref>PMID:11735390</ref> <ref>PMID:22869700</ref> <ref>PMID:2422175</ref> <ref>PMID:3038901</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The T4 bacteriophage gp41 helicase and gp61 primase assemble into a primosome complex to couple DNA unwinding with RNA primer synthesis for DNA replication. How a primosome is assembled and how the length of the RNA primer is defined in the T4 bacteriophage, or in any model system, are unclear. Here we report a series of cryo-EM structures of T4 primosome assembly intermediates at resolutions up to 2.7 A. We show that the gp41 helicase is an open spiral in the absence of ssDNA, and ssDNA binding triggers a large-scale scissor-like conformational change that drives the open spiral to a closed ring that activates the helicase. We found that the activation of the gp41 helicase exposes a cryptic hydrophobic primase-binding surface allowing for the recruitment of the gp61 primase. The primase binds the gp41 helicase in a bipartite mode in which the N-terminal Zn-binding domain (ZBD) and the C-terminal RNA polymerase domain (RPD) each contain a helicase-interacting motif (HIM1 and HIM2, respectively) that bind to separate gp41 N-terminal hairpin dimers, leading to the assembly of one primase on the helicase hexamer. Based on two observed primosome conformations - one in a DNA-scanning mode and the other in a post RNA primer-synthesis mode - we suggest that the linker loop between the gp61 ZBD and RPD contributes to the T4 pentaribonucleotide primer. Our study reveals T4 primosome assembly process and sheds light on RNA primer synthesis mechanism.

-	~~Authors: Feng~~, X., Li, H.	+	Structural basis of the T4 bacteriophage primosome assembly and primer synthesis.,Feng X, Spiering MM, de Luna Almeida Santos R, Benkovic SJ, Li H bioRxiv. 2023 May 3:2023.05.03.539249. doi: 10.1101/2023.05.03.539249. Preprint. PMID:37205424<ref>PMID:37205424</ref>

-	~~Description: Primase~~ of ~~mutant bacteriophage T4 primosome with single strand DNA~~/~~RNA primer hybrid in primer exiting state~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Li, H~~]]	+	<div class="pdbe-citations 8dwj" style="background-color:#fffaf0;"></div>
-	[[Category: Feng, X]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia phage T4]]
		+	[[Category: Large Structures]]
		+	[[Category: Feng X]]
		+	[[Category: Li H]]

OCA: Protected "8dwj" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2022 04:04:42 GMT

Protected "8dwj" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:04, 10 August 2022

OCA: New page: '''Unreleased structure''' The entry 8dwj is ON HOLD Authors: Feng, X., Li, H. Description: Primase of mutant bacteriophage T4 primosome with single strand DNA/RNA primer hybrid in pri...

OCA — Wed, 10 Aug 2022 04:04:41 GMT

New page: '''Unreleased structure''' The entry 8dwj is ON HOLD Authors: Feng, X., Li, H. Description: Primase of mutant bacteriophage T4 primosome with single strand DNA/RNA primer hybrid in pri...

New page

'''Unreleased structure'''

The entry 8dwj is ON HOLD

Authors: Feng, X., Li, H.

Description: Primase of mutant bacteriophage T4 primosome with single strand DNA/RNA primer hybrid in primer exiting state
[[Category: Unreleased Structures]]
[[Category: Li, H]]
[[Category: Feng, X]]