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.

2k47

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution structure of the C-terminal N-RNA binding domain of the Vesicular Stomatitis Virus Phosphoprotein

Structural highlights

2k47 is a 1 chain structure with sequence from Vesicular stomatitis Indiana virus strain San Juan. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHOSP_VSIVA Essential component of the RNA polymerase transcription and replication complex. Binds the viral ribonucleocapsid and positions the L polymerase on the template. May act as a chaperone for newly synthesized free N protein, so-called N(0). Plays a role in virion assembly.^[1] ^[2] ^[3]

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

Beyond common features in their genome organization and replication mechanisms, the evolutionary relationships among viruses of the Rhabdoviridae family are difficult to decipher because of the great variability in the amino acid sequence of their proteins. The phosphoprotein (P) of vesicular stomatitis virus (VSV) is an essential component of the RNA transcription and replication machinery; in particular, it contains binding sites for the RNA-dependent RNA polymerase and for the nucleoprotein. Here, we devised a new method for defining boundaries of structured domains from multiple disorder prediction algorithms, and we identified an autonomous folding C-terminal domain in VSV P (P(CTD)). We show that, like the C-terminal domain of rabies virus (RV) P, VSV P(CTD) binds to the viral nucleocapsid (nucleoprotein-RNA complex). We solved the three-dimensional structure of VSV P(CTD) by NMR spectroscopy and found that the topology of its polypeptide chain resembles that of RV P(CTD). The common part of both proteins could be superimposed with a backbone RMSD from mean atomic coordinates of 2.6 A. VSV P(CTD) has a shorter N-terminal helix (alpha(1)) than RV P(CTD); it lacks two alpha-helices (helices alpha(3) and alpha(6) of RV P), and the loop between strands beta(1) and beta(2) is longer than that in RV. Dynamical properties measured by NMR relaxation revealed the presence of fast motions (below the nanosecond timescale) in loop regions (amino acids 209-214) and slower conformational exchange in the N- and C-terminal helices. Characterization of a longer construct indicated that P(CTD) is preceded by a flexible linker. The results presented here support a modular organization of VSV P, with independent folded domains separated by flexible linkers, which is conserved among different genera of Rhabdoviridae and is similar to that proposed for the P proteins of the Paramyxoviridae.

Solution structure of the C-terminal nucleoprotein-RNA binding domain of the vesicular stomatitis virus phosphoprotein.,Ribeiro EA Jr, Favier A, Gerard FC, Leyrat C, Brutscher B, Blondel D, Ruigrok RW, Blackledge M, Jamin M J Mol Biol. 2008 Oct 3;382(2):525-38. Epub 2008 Jul 16. PMID:18657547^[4]

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

References

↑ Spadafora D, Canter DM, Jackson RL, Perrault J. Constitutive phosphorylation of the vesicular stomatitis virus P protein modulates polymerase complex formation but is not essential for transcription or replication. J Virol. 1996 Jul;70(7):4538-48. PMID:8676480
↑ Das SC, Pattnaik AK. Phosphorylation of vesicular stomatitis virus phosphoprotein P is indispensable for virus growth. J Virol. 2004 Jun;78(12):6420-30. PMID:15163735 doi:http://dx.doi.org/10.1128/JVI.78.12.6420-6430.2004
↑ Das SC, Pattnaik AK. Role of the hypervariable hinge region of phosphoprotein P of vesicular stomatitis virus in viral RNA synthesis and assembly of infectious virus particles. J Virol. 2005 Jul;79(13):8101-12. PMID:15956555 doi:http://dx.doi.org/10.1128/JVI.79.13.8101-8112.2005
↑ Ribeiro EA Jr, Favier A, Gerard FC, Leyrat C, Brutscher B, Blondel D, Ruigrok RW, Blackledge M, Jamin M. Solution structure of the C-terminal nucleoprotein-RNA binding domain of the vesicular stomatitis virus phosphoprotein. J Mol Biol. 2008 Oct 3;382(2):525-38. Epub 2008 Jul 16. PMID:18657547 doi:10.1016/j.jmb.2008.07.028

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/2k47"

@@ Line 1: / Line 1: @@
 ==Solution structure of the C-terminal N-RNA binding domain of the Vesicular Stomatitis Virus Phosphoprotein==
-<StructureSection load='2k47' size='340' side='right' caption='[[2k47]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k47' size='340' side='right'caption='[[2k47]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k47]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vesicular_stomatitis_indiana_virus Vesicular stomatitis indiana virus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K47 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K47 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k47]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vesicular_stomatitis_Indiana_virus_strain_San_Juan Vesicular stomatitis Indiana virus strain San Juan]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K47 FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">P ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11277 Vesicular stomatitis Indiana virus])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2k47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k47 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k47 RCSB], [http://www.ebi.ac.uk/pdbsum/2k47 PDBsum]</span></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=2k47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k47 OCA], [https://pdbe.org/2k47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k47 RCSB], [https://www.ebi.ac.uk/pdbsum/2k47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k47 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHOSP_VSIVA PHOSP_VSIVA]] Essential component of the RNA polymerase transcription and replication complex. Binds the viral ribonucleocapsid and positions the L polymerase on the template. May act as a chaperone for newly synthesized free N protein, so-called N(0). Plays a role in virion assembly.<ref>PMID:8676480</ref> <ref>PMID:15163735</ref> <ref>PMID:15956555</ref>
+[https://www.uniprot.org/uniprot/PHOSP_VSIVA PHOSP_VSIVA] Essential component of the RNA polymerase transcription and replication complex. Binds the viral ribonucleocapsid and positions the L polymerase on the template. May act as a chaperone for newly synthesized free N protein, so-called N(0). Plays a role in virion assembly.<ref>PMID:8676480</ref> <ref>PMID:15163735</ref> <ref>PMID:15956555</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/k4/2k47_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/2k47_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=2k47 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2k47" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Vesicular stomatitis indiana virus]]
+[[Category: Large Structures]]
-[[Category: Blackledge, M]]
+[[Category: Vesicular stomatitis Indiana virus strain San Juan]]
-[[Category: Blondel, D]]
+[[Category: Blackledge M]]
-[[Category: Brutscher, B]]
+[[Category: Blondel D]]
-[[Category: Favier, A]]
+[[Category: Brutscher B]]
-[[Category: Gerard, F C]]
+[[Category: Favier A]]
-[[Category: Jamin, M]]
+[[Category: Gerard FC]]
-[[Category: Leyrat, C]]
+[[Category: Jamin M]]
-[[Category: Ribeiro, E A]]
+[[Category: Leyrat C]]
-[[Category: Ruigrok, R W]]
+[[Category: Ribeiro EA]]
-[[Category: Chaperone]]
+[[Category: Ruigrok RW]]
-[[Category: Flexible tail]]
-[[Category: Phosphoprotein]]
-[[Category: Replication]]
-[[Category: Rna replication]]
-[[Category: Virion]]

2k47

From Proteopedia

Current revision

Solution structure of the C-terminal N-RNA binding domain of the Vesicular Stomatitis Virus Phosphoprotein

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