2ofz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2ofz" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ofz, resolution 1.17&Aring;" /> '''Ultrahigh Resolution...)
Current revision (10:37, 30 August 2023) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ofz.jpg|left|200px]]<br /><applet load="2ofz" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2ofz, resolution 1.17&Aring;" />
 
-
'''Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.'''<br />
 
-
==Overview==
+
==Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.==
-
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.
+
<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 [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='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='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'>[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 ==
 +
[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>
 +
<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/main_output.php?pdb_ID=2ofz ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
==About this Structure==
+
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<ref>PMID:17229691</ref>
-
2OFZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sars_coronavirus Sars coronavirus] with EDO as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2OFZ OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17229691 17229691]
+
</div>
-
[[Category: Sars coronavirus]]
+
<div class="pdbe-citations 2ofz" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Buchmeier, M.]]
+
-
[[Category: Joseph, J.]]
+
-
[[Category: Kuhn, P.]]
+
-
[[Category: Neuman, B.]]
+
-
[[Category: Saikatendu, K.]]
+
-
[[Category: Stevens, R.C.]]
+
-
[[Category: Subramanian, V.]]
+
-
[[Category: EDO]]
+
-
[[Category: n protein]]
+
-
[[Category: sars coronavirus nucleocapsid rna binding n-terminal domain]]
+
-
[[Category: sars-orf9a]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:09:41 2007''
+
==See Also==
 +
*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: SARS coronavirus Tor2]]
 +
[[Category: Buchmeier M]]
 +
[[Category: Joseph J]]
 +
[[Category: Kuhn P]]
 +
[[Category: Neuman B]]
 +
[[Category: Saikatendu K]]
 +
[[Category: Stevens RC]]
 +
[[Category: Subramanian V]]

Current revision

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

PDB ID 2ofz

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

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