This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1qbe

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

BACTERIOPHAGE Q BETA CAPSID

Structural highlights

1qbe 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:	X-ray diffraction, Resolution 3.5Å
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

BACKGROUND: The capsid protein subunits of small RNA bacteriophages form a T = 3 particle upon assembly and RNA encapsidation. Dimers of the capsid protein repress translation of the replicase gene product by binding to the ribosome binding site and this interaction is believed to initiate RNA encapsidation. We have determined the crystal structure of phage Q beta with the aim of clarifying which factors are the most important for particle assembly and RNA interaction in the small phages. RESULTS: The crystal structure of bacteriophage Q beta determined at 3.5 A resolution shows that the capsid is stabilized by disulfide bonds on each side of the flexible loops that are situated around the fivefold and quasi-sixfold axes. As in other small RNA phages, the protein capsid is constructed from subunits which associate into dimers. A contiguous ten-stranded antiparallel beta sheet facing the RNA is formed in the dimer. The disulfide bonds lock the constituent dimers of the capsid covalently in the T = 3 lattice. CONCLUSIONS: The unusual stability of the Q beta particle is due to the tight dimer interactions and the disulfide bonds linking each dimer covalently to the rest of the capsid. A comparison with the structure of the related phage MS2 shows that although the fold of the Q beta coat protein is very similar, the details of the protein-protein interactions are completely different. The most conserved region of the protein is at the surface, which, in MS2, is involved in RNA binding.

The crystal structure of bacteriophage Q beta at 3.5 A resolution.,Golmohammadi R, Fridborg K, Bundule M, Valegard K, Liljas L Structure. 1996 May 15;4(5):543-54. PMID:8736553^[5]

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

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
↑ Golmohammadi R, Fridborg K, Bundule M, Valegard K, Liljas L. The crystal structure of bacteriophage Q beta at 3.5 A resolution. Structure. 1996 May 15;4(5):543-54. PMID:8736553

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1qbe"

Categories: Escherichia virus Qbeta | Large Structures | Golmohammadi R | Liljas L

@@ Line 1: / Line 1: @@
 ==BACTERIOPHAGE Q BETA CAPSID==
-<StructureSection load='1qbe' size='340' side='right' caption='[[1qbe]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<StructureSection load='1qbe' size='340' side='right'caption='[[1qbe]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1qbe]] 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=1QBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QBE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1qbe]] 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=1QBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QBE 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=1qbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qbe RCSB], [http://www.ebi.ac.uk/pdbsum/1qbe PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#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=1qbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qbe OCA], [https://pdbe.org/1qbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qbe RCSB], [https://www.ebi.ac.uk/pdbsum/1qbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qbe 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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbe_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/1qbe_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1qbe ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1qbe" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Enterobacteria phage qbeta]]
+[[Category: Escherichia virus Qbeta]]
-[[Category: Golmohammadi, R]]
+[[Category: Large Structures]]
-[[Category: Liljas, L]]
+[[Category: Golmohammadi R]]
-[[Category: Coat protein]]
+[[Category: Liljas L]]
-[[Category: Icosahedral virus]]
-[[Category: Rna binding]]
-[[Category: Virus]]

1qbe

From Proteopedia

Current revision

BACTERIOPHAGE Q BETA CAPSID

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox