8pe4

From Proteopedia

(Difference between revisions)

Current revision

Capsid structure of the L-A helper virus from native viral communities

Structural highlights

8pe4 is a 2 chain structure with sequence from Saccharomyces cerevisiae virus L-A. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.21Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GAG_SCVLA Capsid protein self-assembles to form an icosahedral capsid with a T=2 symmetry, 40 nm in diameter, and consisting of 60 capsid proteins asymmetric dimers. The capsid encapsulates the genomic dsRNA and the polymerase and remains intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of the virion and are extruded into the cytoplasm.^[1] ^[2] Binds and removes 5' cap structures from cellular mRNA. Forms a covalent bond with m7GMP through His-154 of the capsid protein while releasing the mRNA body.^[3] ^[4]

Publication Abstract from PubMed

The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-pi stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.

Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts.,Schmidt L, Tuting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL Commun Biol. 2024 May 10;7(1):557. doi: 10.1038/s42003-024-06204-7. PMID:38730276^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Blanc A, Goyer C, Sonenberg N. The coat protein of the yeast double-stranded RNA virus L-A attaches covalently to the cap structure of eukaryotic mRNA. Mol Cell Biol. 1992 Aug;12(8):3390-8. PMID:1630453
↑ Masison DC, Blanc A, Ribas JC, Carroll K, Sonenberg N, Wickner RB. Decoying the cap- mRNA degradation system by a double-stranded RNA virus and poly(A)- mRNA surveillance by a yeast antiviral system. Mol Cell Biol. 1995 May;15(5):2763-71. PMID:7739557
↑ Blanc A, Goyer C, Sonenberg N. The coat protein of the yeast double-stranded RNA virus L-A attaches covalently to the cap structure of eukaryotic mRNA. Mol Cell Biol. 1992 Aug;12(8):3390-8. PMID:1630453
↑ Masison DC, Blanc A, Ribas JC, Carroll K, Sonenberg N, Wickner RB. Decoying the cap- mRNA degradation system by a double-stranded RNA virus and poly(A)- mRNA surveillance by a yeast antiviral system. Mol Cell Biol. 1995 May;15(5):2763-71. PMID:7739557
↑ Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol. 2024 May 10;7(1):557. PMID:38730276 doi:10.1038/s42003-024-06204-7

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/8pe4"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8pe4 is ON HOLD  until Paper Publication
+==Capsid structure of the L-A helper virus from native viral communities==
+<StructureSection load='8pe4' size='340' side='right'caption='[[8pe4]], [[Resolution|resolution]] 3.21&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8pe4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_virus_L-A Saccharomyces cerevisiae virus L-A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8PE4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8PE4 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.21&#8491;</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=8pe4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8pe4 OCA], [https://pdbe.org/8pe4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8pe4 RCSB], [https://www.ebi.ac.uk/pdbsum/8pe4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8pe4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GAG_SCVLA GAG_SCVLA] Capsid protein self-assembles to form an icosahedral capsid with a T=2 symmetry, 40 nm in diameter, and consisting of 60 capsid proteins asymmetric dimers. The capsid encapsulates the genomic dsRNA and the polymerase and remains intact following cell entry to protect the dsRNA from degradation and to prevent unfavorable antiviral responses in the host cell during all the replication cycle of the virus. Nacent transcripts are transcribed within the structural confines of the virion and are extruded into the cytoplasm.<ref>PMID:1630453</ref> <ref>PMID:7739557</ref>   Binds and removes 5' cap structures from cellular mRNA. Forms a covalent bond with m7GMP through His-154 of the capsid protein while releasing the mRNA body.<ref>PMID:1630453</ref> <ref>PMID:7739557</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-pi stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.
-Authors:
+Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts.,Schmidt L, Tuting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL Commun Biol. 2024 May 10;7(1):557. doi: 10.1038/s42003-024-06204-7. PMID:38730276<ref>PMID:38730276</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 8pe4" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Saccharomyces cerevisiae virus L-A]]
+[[Category: Kastritis PL]]
+[[Category: Schmidt L]]
+[[Category: Stubbs MT]]
+[[Category: Tueting C]]

8pe4

From Proteopedia

Current revision

Capsid structure of the L-A helper virus from native viral communities

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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