2ofz

From Proteopedia

(Difference between revisions)

Current revision

Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.

Structural highlights

2ofz is a 1 chain structure with sequence from SARS coronavirus Tor2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.17Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NCAP_SARS Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication (PubMed:17210170). May modulate transforming growth factor-beta signaling by binding host SMAD3 (PubMed:18055455).[HAMAP-Rule:MF_04096]^[1] ^[2]

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

Conserved among all coronaviruses are four structural proteins: the matrix (M), small envelope (E), and spike (S) proteins that are embedded in the viral membrane and the nucleocapsid phosphoprotein (N), which exists in a ribonucleoprotein complex in the lumen. The N-terminal domain of coronaviral N proteins (N-NTD) provides a scaffold for RNA binding, while the C-terminal domain (N-CTD) mainly acts as oligomerization modules during assembly. The C terminus of the N protein anchors it to the viral membrane by associating with M protein. We characterized the structures of N-NTD from severe acute respiratory syndrome coronavirus (SARS-CoV) in two crystal forms, at 1.17 A (monoclinic) and at 1.85 A (cubic), respectively, resolved by molecular replacement using the homologous avian infectious bronchitis virus (IBV) structure. Flexible loops in the solution structure of SARS-CoV N-NTD are now shown to be well ordered around the beta-sheet core. The functionally important positively charged beta-hairpin protrudes out of the core, is oriented similarly to that in the IBV N-NTD, and is involved in crystal packing in the monoclinic form. In the cubic form, the monomers form trimeric units that stack in a helical array. Comparison of crystal packing of SARS-CoV and IBV N-NTDs suggests a common mode of RNA recognition, but they probably associate differently in vivo during the formation of the ribonucleoprotein complex. Electrostatic potential distribution on the surface of homology models of related coronaviral N-NTDs suggests that they use different modes of both RNA recognition and oligomeric assembly, perhaps explaining why their nucleocapsids have different morphologies.

Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein.,Saikatendu KS, Joseph JS, Subramanian V, Neuman BW, Buchmeier MJ, Stevens RC, Kuhn P J Virol. 2007 Apr;81(8):3913-21. Epub 2007 Jan 17. PMID:17229691^[3]

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

References

↑ Stertz S, Reichelt M, Spiegel M, Kuri T, Martínez-Sobrido L, García-Sastre A, Weber F, Kochs G. The intracellular sites of early replication and budding of SARS-coronavirus. Virology. 2007 May 10;361(2):304-15. PMID:17210170 doi:10.1016/j.virol.2006.11.027
↑ Zhao X, Nicholls JM, Chen YG. Severe acute respiratory syndrome-associated coronavirus nucleocapsid protein interacts with Smad3 and modulates transforming growth factor-beta signaling. J Biol Chem. 2008 Feb 8;283(6):3272-3280. PMID:18055455 doi:10.1074/jbc.M708033200
↑ Saikatendu KS, Joseph JS, Subramanian V, Neuman BW, Buchmeier MJ, Stevens RC, Kuhn P. Ribonucleocapsid formation of severe acute respiratory syndrome coronavirus through molecular action of the N-terminal domain of N protein. J Virol. 2007 Apr;81(8):3913-21. Epub 2007 Jan 17. PMID:17229691 doi:10.1128/JVI.02236-06

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ofz"

@@ Line 1: / Line 1: @@
 ==Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.==
-<StructureSection load='2ofz' size='340' side='right' caption='[[2ofz]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
+<StructureSection load='2ofz' size='340' side='right'caption='[[2ofz]], [[Resolution|resolution]] 1.17&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ofz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus_tor2 Sars coronavirus tor2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OFZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OFZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ofz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/SARS_coronavirus_Tor2 SARS coronavirus Tor2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OFZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OFZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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]] 1.17&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">N ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227984 SARS coronavirus Tor2])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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=2ofz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ofz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ofz RCSB], [http://www.ebi.ac.uk/pdbsum/2ofz 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=2ofz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ofz OCA], [https://pdbe.org/2ofz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ofz RCSB], [https://www.ebi.ac.uk/pdbsum/2ofz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ofz ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/NCAP_CVHSA NCAP_CVHSA]] Major structural component of virions that associates with genomic RNA to form a long, flexible, helical nucleocapsid (By similarity).
+[https://www.uniprot.org/uniprot/NCAP_SARS NCAP_SARS] Packages the positive strand viral genome RNA into a helical ribonucleocapsid (RNP) and plays a fundamental role during virion assembly through its interactions with the viral genome and membrane protein M. Plays an important role in enhancing the efficiency of subgenomic viral RNA transcription as well as viral replication (PubMed:17210170). May modulate transforming growth factor-beta signaling by binding host SMAD3 (PubMed:18055455).[HAMAP-Rule:MF_04096]<ref>PMID:17210170</ref> <ref>PMID:18055455</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/of/2ofz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/of/2ofz_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=2ofz ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2ofz" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Nucleoprotein|Nucleoprotein]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Sars coronavirus tor2]]
+[[Category: Large Structures]]
-[[Category: Buchmeier, M]]
+[[Category: SARS coronavirus Tor2]]
-[[Category: Joseph, J]]
+[[Category: Buchmeier M]]
-[[Category: Kuhn, P]]
+[[Category: Joseph J]]
-[[Category: Neuman, B]]
+[[Category: Kuhn P]]
-[[Category: Saikatendu, K]]
+[[Category: Neuman B]]
-[[Category: Stevens, R C]]
+[[Category: Saikatendu K]]
-[[Category: Subramanian, V]]
+[[Category: Stevens RC]]
-[[Category: N protein]]
+[[Category: Subramanian V]]
-[[Category: Sars coronavirus nucleocapsid rna binding n-terminal domain]]
-[[Category: Sars-orf9a]]
-[[Category: Viral protein]]

2ofz

From Proteopedia

Current revision

Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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