5kip: Difference between revisions

Latest revision as of 15:40, 6 March 2024

Asymmetric unit for the coat proteins of phage QbetaAsymmetric unit for the coat proteins of phage Qbeta

5kip, resolution 3.70Å

Structural highlights

5kip is a 3 chain structure with sequence from Escherichia virus Qbeta. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.7Å
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BPQBE Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 26 nm in diameter, and consisting of 89 capsid proteins dimers (178 capsid proteins) (PubMed:27671640, PubMed:19913556). Involved in viral genome encapsidation through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome (PubMed:8943226, PubMed:27671640). Binding of the capsid proteins to the viral RNA induces a conformational change required for efficient T=3 shell formation (PubMed:19913556). The capsid contains also 1 copy of the A2 maturation protein (PubMed:27671640).^[1] ^[2] ^[3] Acts as a translational repressor of viral replicase synthesis late in infection. This latter function is the result of capsid protein interaction with an RNA hairpin which contains the replicase ribosome-binding site.^[4]

References

↑ Basnak G, Morton VL, Rolfsson O, Stonehouse NJ, Ashcroft AE, Stockley PG. Viral genomic single-stranded RNA directs the pathway toward a T=3 capsid. J Mol Biol. 2010 Feb 5;395(5):924-36. doi: 10.1016/j.jmb.2009.11.018. Epub 2009, Nov 12. PMID:19913556 doi:http://dx.doi.org/10.1016/j.jmb.2009.11.018
↑ Gorzelnik KV, Cui Z, Reed CA, Jakana J, Young R, Zhang J. Asymmetric cryo-EM structure of the canonical Allolevivirus Qbeta reveals a single maturation protein and the genomic ssRNA in situ. Proc Natl Acad Sci U S A. 2016 Sep 26. pii: 201609482. PMID:27671640 doi:http://dx.doi.org/10.1073/pnas.1609482113
↑ Lim F, Spingola M, Peabody DS. The RNA-binding site of bacteriophage Qbeta coat protein. J Biol Chem. 1996 Dec 13;271(50):31839-45. PMID:8943226
↑ Lim F, Spingola M, Peabody DS. The RNA-binding site of bacteriophage Qbeta coat protein. J Biol Chem. 1996 Dec 13;271(50):31839-45. PMID:8943226

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OCA

[1] Basnak G, Morton VL, Rolfsson O, Stonehouse NJ, Ashcroft AE, Stockley PG. Viral genomic single-stranded RNA directs the pathway toward a T=3 capsid. J Mol Biol. 2010 Feb 5;395(5):924-36. doi: 10.1016/j.jmb.2009.11.018. Epub 2009, Nov 12. PMID:19913556 doi:http://dx.doi.org/10.1016/j.jmb.2009.11.018

[2] Gorzelnik KV, Cui Z, Reed CA, Jakana J, Young R, Zhang J. Asymmetric cryo-EM structure of the canonical Allolevivirus Qbeta reveals a single maturation protein and the genomic ssRNA in situ. Proc Natl Acad Sci U S A. 2016 Sep 26. pii: 201609482. PMID:27671640 doi:http://dx.doi.org/10.1073/pnas.1609482113

[3] Lim F, Spingola M, Peabody DS. The RNA-binding site of bacteriophage Qbeta coat protein. J Biol Chem. 1996 Dec 13;271(50):31839-45. PMID:8943226

[4] Lim F, Spingola M, Peabody DS. The RNA-binding site of bacteriophage Qbeta coat protein. J Biol Chem. 1996 Dec 13;271(50):31839-45. PMID:8943226

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Asymmetric unit for the coat proteins of phage Qbeta==
-<StructureSection load='5kip' size='340' side='right' caption='[[5kip]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+<SX load='5kip' size='340' side='right' viewer='molstar' caption='[[5kip]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kip]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_qbeta Enterobacteria phage qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KIP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kip]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Qbeta Escherichia virus Qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KIP 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=5kip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kip OCA], [http://pdbe.org/5kip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kip RCSB], [http://www.ebi.ac.uk/pdbsum/5kip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kip ProSAT]</span></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]] 3.7&#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=5kip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kip OCA], [https://pdbe.org/5kip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kip RCSB], [https://www.ebi.ac.uk/pdbsum/5kip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kip ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/COAT_BPQBE COAT_BPQBE]] Forms the phage shell; binds to the phage RNA.
+[https://www.uniprot.org/uniprot/CAPSD_BPQBE CAPSD_BPQBE] Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 26 nm in diameter, and consisting of 89 capsid proteins dimers (178 capsid proteins) (PubMed:27671640, PubMed:19913556). Involved in viral genome encapsidation through the interaction between a capsid protein dimer and the multiple packaging signals present in the RNA genome (PubMed:8943226, PubMed:27671640). Binding of the capsid proteins to the viral RNA induces a conformational change required for efficient T=3 shell formation (PubMed:19913556). The capsid contains also 1 copy of the A2 maturation protein (PubMed:27671640).<ref>PMID:19913556</ref> <ref>PMID:27671640</ref> <ref>PMID:8943226</ref>   Acts as a translational repressor of viral replicase synthesis late in infection. This latter function is the result of capsid protein interaction with an RNA hairpin which contains the replicase ribosome-binding site.<ref>PMID:8943226</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Single-stranded (ss) RNA viruses infect all domains of life. To date, for most ssRNA virions, only the structures of the capsids and their associated protein components have been resolved to high resolution. Qbeta, an ssRNA phage specific for the conjugative F-pilus, has a T = 3 icosahedral lattice of coat proteins assembled around its 4,217 nucleotides of genomic RNA (gRNA). In the mature virion, the maturation protein, A2, binds to the gRNA and is required for adsorption to the F-pilus. Here, we report the cryo-electron microscopy (cryo-EM) structures of Qbeta with and without symmetry applied. The icosahedral structure, at 3.7-A resolution, resolves loops not previously seen in the published X-ray structure, whereas the asymmetric structure, at 7-A resolution, reveals A2 and the gRNA. A2 contains a bundle of alpha-helices and replaces one dimer of coat proteins at a twofold axis. The helix bundle binds gRNA, causing denser packing of RNA in its proximity, which asymmetrically expands the surrounding coat protein shell to potentially facilitate RNA release during infection. We observe a fixed pattern of gRNA organization among all viral particles, with the major and minor grooves of RNA helices clearly visible. A single layer of RNA directly contacts every copy of the coat protein, with one-third of the interactions occurring at operator-like RNA hairpins. These RNA-coat interactions stabilize the tertiary structure of gRNA within the virion, which could further provide a roadmap for capsid assembly.
-Asymmetric cryo-EM structure of the canonical Allolevivirus Qbeta reveals a single maturation protein and the genomic ssRNA in situ.,Gorzelnik KV, Cui Z, Reed CA, Jakana J, Young R, Zhang J Proc Natl Acad Sci U S A. 2016 Sep 26. pii: 201609482. PMID:27671640<ref>PMID:27671640</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5kip" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Virus coat protein|Virus coat protein]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
-[[Category: Enterobacteria phage qbeta]]
+[[Category: Escherichia virus Qbeta]]
-[[Category: Cui, Z]]
+[[Category: Large Structures]]
-[[Category: Gorzelnik, K V]]
+[[Category: Cui Z]]
-[[Category: Zhang, J]]
+[[Category: Gorzelnik KV]]
-[[Category: Phage]]
+[[Category: Zhang J]]
-[[Category: Qbeta]]
-[[Category: Ssrna]]
-[[Category: Virus]]

5kip: Difference between revisions

Latest revision as of 15:40, 6 March 2024

Asymmetric unit for the coat proteins of phage QbetaAsymmetric unit for the coat proteins of phage Qbeta

Structural highlights

Function

References

Contents

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5kip: Difference between revisions

Latest revision as of 15:40, 6 March 2024

Asymmetric unit for the coat proteins of phage QbetaAsymmetric unit for the coat proteins of phage Qbeta

Structural highlights

Function

References

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