We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

4v4m

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 08:03, 29 March 2023

1.45 Angstrom Structure of STNV coat protein

Structural highlights

4v4m is a 60 chain structure with sequence from Satellite tobacco necrosis virus 1. This structure supersedes the now removed PDB entries 1vtz and 3rqv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_STNV1 Self-assembles to form an icosahedral capsid of 17 nm in diameter.^[1] ^[2] ^[3]

Publication Abstract from PubMed

A codon-optimised gene has been expressed in Escherichia coli to produce the coat protein (CP) of the Satellite Tobacco Necrosis Virus. This protein assembles in vivo into capsids closely resembling those of the T=1 wild-type virus. These virus-like particles (VLPs) package the recombinant mRNA transcript and can be disassembled and reassembled using different buffer conditions. The X-ray crystal structure of the VLP has been solved and refined at 1.4 A resolution and shown to be very similar to that of wild-type Satellite Tobacco Necrosis Virus, except that icosahedral symmetry constraints could be removed to reveal differences between subunits, presumably owing to crystal packing. An additional low-resolution X-ray crystal structure determination revealed well-ordered RNA fragments lodged near the inside surface of the capsid, close to basic clusters formed by the N-terminal helices that project into the interior of the particle. The RNA consists of multiple copies of a 3-bp helical stem, with a single unpaired base at the 3' end, and probably consists of a number of short stem-loops where the loop region is disordered. The arrangement of the RNA is different from that observed in other satellite viruses.

Construction and Crystal Structure of Recombinant STNV Capsids.,Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE J Mol Biol. 2011 Oct 14;413(1):41-50. Epub 2011 Aug 3. PMID:21839089^[4]

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

References

↑ Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE. Construction and Crystal Structure of Recombinant STNV Capsids. J Mol Biol. 2011 Oct 14;413(1):41-50. Epub 2011 Aug 3. PMID:21839089 doi:10.1016/j.jmb.2011.07.062
↑ Ford RJ, Barker AM, Bakker SE, Coutts RH, Ranson NA, Phillips SE, Pearson AR, Stockley PG. Sequence-Specific, RNA-Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein. J Mol Biol. 2013 Jan 11. pii: S0022-2836(13)00007-7. doi:, 10.1016/j.jmb.2013.01.004. PMID:23318955 doi:http://dx.doi.org/10.1016/j.jmb.2013.01.004
↑ Jones TA, Liljas L. Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 A resolution. J Mol Biol. 1984 Aug 25;177(4):735-67. PMID:6481804
↑ Lane SW, Dennis CA, Lane CL, Trinh CH, Rizkallah PJ, Stockley PG, Phillips SE. Construction and Crystal Structure of Recombinant STNV Capsids. J Mol Biol. 2011 Oct 14;413(1):41-50. Epub 2011 Aug 3. PMID:21839089 doi:10.1016/j.jmb.2011.07.062

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4v4m"

@@ Line 3: / Line 3: @@
 <StructureSection load='4v4m' size='340' side='right'caption='[[4v4m]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v4m]] is a 60 chain structure with sequence from [http://en.wikipedia.org/wiki/Stnv1 Stnv1]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vtz 1vtz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rqv 3rqv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V4M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v4m]] is a 60 chain structure with sequence from [https://en.wikipedia.org/wiki/Satellite_tobacco_necrosis_virus_1 Satellite tobacco necrosis virus 1]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1vtz 1vtz] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rqv 3rqv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V4M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V4M FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3s4g|3s4g]]</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=4v4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4m OCA], [https://pdbe.org/4v4m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v4m RCSB], [https://www.ebi.ac.uk/pdbsum/4v4m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4m ProSAT]</span></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=4v4m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v4m OCA], [http://pdbe.org/4v4m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v4m RCSB], [http://www.ebi.ac.uk/pdbsum/4v4m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v4m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_STNV1 CAPSD_STNV1] Self-assembles to form an icosahedral capsid of 17 nm in diameter.<ref>PMID:21839089</ref> <ref>PMID:23318955</ref> <ref>PMID:6481804</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 ==See Also==
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Stnv1]]
+[[Category: Satellite tobacco necrosis virus 1]]
-[[Category: Dennis, C A]]
+[[Category: Dennis CA]]
-[[Category: Lane, C L]]
+[[Category: Lane CL]]
-[[Category: Lane, S W]]
+[[Category: Lane SW]]
-[[Category: Phillips, S E.V]]
+[[Category: Phillips SEV]]
-[[Category: Rizkallah, P J]]
+[[Category: Rizkallah PJ]]
-[[Category: Stockley, P G]]
+[[Category: Stockley PG]]
-[[Category: Trinh, C H]]
+[[Category: Trinh CH]]
-[[Category: Coat protein]]
-[[Category: Jelly-roll beta-sandwich]]
-[[Category: Virus]]

4v4m

From Proteopedia

Revision as of 08:03, 29 March 2023

1.45 Angstrom Structure of STNV coat protein

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox