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4v99

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Revision as of 14:31, 10 April 2020

The Crystallographic Structure of Panicum Mosaic Virus

Structural highlights

4v99 is a 480 chain structure with sequence from Panicum mosaic virus. This structure supersedes the now removed PDB entries 4fy1, 4fy2, 4fy3, 4fy4, 4fy5, 4fy6, 4fy7, 4fy8, 4fy9 and 4fya. 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_PMVK] Capsid protein self-assembles to form an icosahedral capsid with a T=3 symmetry, about 32-35 nm in diameter, and consisting of 180 capsid proteins.

Publication Abstract from PubMed

The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9A resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7A, b=403.9A and c=412.5A, with beta=89.7 degrees . The asymmetric unit was two entire T=3 virus particles, or 360 protein subunits. The structure was solved by conventional molecular replacement from two distant homologues, Cocksfoot Mottle Virus (CfMV) and Tobacco Necrosis Virus (TNV), of approximately 20% sequence identity followed by phase extension. The model was initially refined with exact icosahedral constraints and then with icosahedral restraints. The virus has Ca(++) ions octahedrally coordinated by six aspartic acid residues on quasi threefold axes, which is completely different than for either CfMV or TNV. Amino terminal residues 1-53, 1-49 and 1-21 of the A, B and C subunits, respectively, and the four C-terminal residues (239-242) are not visible in electron density maps. The additional ordered residues of the C chain form a prominent "arm" that intertwines with symmetry equivalent "arms" at icosahedral threefold axes, as was seen in both CfMV and TNV. A 17 nucleotide hairpin segment of genomic RNA is icosahedrally ordered and bound at 60 equivalent sites at quasi twofold A-B subunit interfaces at the interior surface of the capsid. This segment of RNA may serve as a conformational switch for coat protein subunits, as has been proposed for similar RNA segments in other viruses.

The crystallographic structure of Panicum Mosaic Virus (PMV).,Makino DL, Larson SB, McPherson A J Struct Biol. 2012 Nov 1. pii: S1047-8477(12)00294-8. doi:, 10.1016/j.jsb.2012.10.012. PMID:23123270^[1]

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

References

↑ Makino DL, Larson SB, McPherson A. The crystallographic structure of Panicum Mosaic Virus (PMV). J Struct Biol. 2012 Nov 1. pii: S1047-8477(12)00294-8. doi:, 10.1016/j.jsb.2012.10.012. PMID:23123270 doi:http://dx.doi.org/10.1016/j.jsb.2012.10.012

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/4v99"

@@ Line 3: / Line 3: @@
 <StructureSection load='4v99' size='340' side='right'caption='[[4v99]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4v99]] is a 480 chain structure with sequence from [http://en.wikipedia.org/wiki/Panicum_mosaic_virus Panicum mosaic virus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy1 4fy1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy2 4fy2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy3 4fy3], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy4 4fy4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy5 4fy5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy6 4fy6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy7 4fy7], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy8 4fy8], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy9 4fy9] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fya 4fya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V99 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V99 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4v99]] is a 480 chain structure with sequence from [http://en.wikipedia.org/wiki/Panicum_mosaic_virus Panicum mosaic virus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy1 4fy1], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy2 4fy2], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy3 4fy3], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy4 4fy4], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy5 4fy5], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy6 4fy6], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy7 4fy7], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy8 4fy8], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fy9 4fy9] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4fya 4fya]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V99 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4V99 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='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=4v99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v99 OCA], [http://pdbe.org/4v99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v99 RCSB], [http://www.ebi.ac.uk/pdbsum/4v99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v99 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4v99 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v99 OCA], [http://pdbe.org/4v99 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v99 RCSB], [http://www.ebi.ac.uk/pdbsum/4v99 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v99 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Virus coat protein|Virus coat protein]]
+*[[Virus coat proteins 3D structures|Virus coat proteins 3D structures]]
 == References ==
 <references/>

4v99

From Proteopedia

Revision as of 14:31, 10 April 2020

The Crystallographic Structure of Panicum Mosaic Virus

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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