2vwd

From Proteopedia

(Difference between revisions)

Current revision

Nipah Virus Attachment Glycoprotein

Structural highlights

2vwd is a 2 chain structure with sequence from Henipavirus nipahense. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.25Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GLYCP_NIPAV Interacts with host ephrinB2/EFNB2 or ephrin B3/EFNB3 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis.^[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

Two members of the paramyxovirus family, Nipah virus (NiV) and Hendra virus (HeV), are recent additions to a growing number of agents of emergent diseases which use bats as a natural host. Identification of ephrin-B2 and ephrin-B3 as cellular receptors for these viruses has enabled the development of immunotherapeutic reagents which prevent virus attachment and subsequent fusion. Here we present the structural analysis of the protein and carbohydrate components of the unbound viral attachment glycoprotein of NiV glycoprotein (NiV-G) at a 2.2-A resolution. Comparison with its ephrin-B2-bound form reveals that conformational changes within the envelope glycoprotein are required to achieve viral attachment. Structural differences are particularly pronounced in the 579-590 loop, a major component of the ephrin binding surface. In addition, the 236-245 loop is rather disordered in the unbound structure. We extend our structural characterization of NiV-G with mass spectrometric analysis of the carbohydrate moieties. We demonstrate that NiV-G is largely devoid of the oligomannose-type glycans that in viruses such as human immunodeficiency virus type 1 and Ebola virus influence viral tropism and the host immune response. Nevertheless, we find putative ligands for the endothelial cell lectin, LSECtin. Finally, by mapping structural conservation and glycosylation site positions from other members of the paramyxovirus family, we suggest the molecular surface involved in oligomerization. These results suggest possible pathways of virus-host interaction and strategies for the optimization of recombinant vaccines.

Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design.,Bowden TA, Crispin M, Harvey DJ, Aricescu AR, Grimes JM, Jones EY, Stuart DI J Virol. 2008 Dec;82(23):11628-36. Epub 2008 Sep 24. PMID:18815311^[3]

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

References

↑ Diederich S, Maisner A. Molecular characteristics of the Nipah virus glycoproteins. Ann N Y Acad Sci. 2007 Apr;1102:39-50. PMID:17470910 doi:http://dx.doi.org/10.1196/annals.1408.003
↑ Diederich S, Moll M, Klenk HD, Maisner A. The nipah virus fusion protein is cleaved within the endosomal compartment. J Biol Chem. 2005 Aug 19;280(33):29899-903. Epub 2005 Jun 16. PMID:15961384 doi:http://dx.doi.org/10.1074/jbc.M504598200
↑ Bowden TA, Crispin M, Harvey DJ, Aricescu AR, Grimes JM, Jones EY, Stuart DI. Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design. J Virol. 2008 Dec;82(23):11628-36. Epub 2008 Sep 24. PMID:18815311 doi:10.1128/JVI.01344-08

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/2vwd"

@@ Line 1: / Line 1: @@
-==NIPAH VIRUS ATTACHMENT GLYCOPROTEIN==
-<StructureSection load='2vwd' size='340' side='right' caption='[[2vwd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+==Nipah Virus Attachment Glycoprotein==
+<StructureSection load='2vwd' size='340' side='right'caption='[[2vwd]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vwd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Nipah_virus Nipah virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VWD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vwd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Henipavirus_nipahense Henipavirus nipahense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VWD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VWD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GBL:GAMMA-BUTYROLACTONE'>GBL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.25&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2vsm|2vsm]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GBL:GAMMA-BUTYROLACTONE'>GBL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2vwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vwd RCSB], [http://www.ebi.ac.uk/pdbsum/2vwd 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=2vwd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vwd OCA], [https://pdbe.org/2vwd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vwd RCSB], [https://www.ebi.ac.uk/pdbsum/2vwd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vwd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/GLYCP_NIPAV GLYCP_NIPAV]] Interacts with host ephrinB2/EFNB2 or ephrin B3/EFNB3 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis.<ref>PMID:17470910</ref> <ref>PMID:15961384</ref>
+[https://www.uniprot.org/uniprot/GLYCP_NIPAV GLYCP_NIPAV] Interacts with host ephrinB2/EFNB2 or ephrin B3/EFNB3 to provide virion attachment to target cell. This attachment induces virion internalization predominantly through clathrin-mediated endocytosis.<ref>PMID:17470910</ref> <ref>PMID:15961384</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/vw/2vwd_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vw/2vwd_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2vwd 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 2vwd" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Hemagglutinin|Hemagglutinin]]
+*[[Hemagglutinin 3D structures|Hemagglutinin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Nipah virus]]
+[[Category: Henipavirus nipahense]]
-[[Category: Aricescu, A R]]
+[[Category: Large Structures]]
-[[Category: Bowden, T A]]
+[[Category: Aricescu AR]]
-[[Category: Crispin, M]]
+[[Category: Bowden TA]]
-[[Category: Grimes, J M]]
+[[Category: Crispin M]]
-[[Category: Harvey, D J]]
+[[Category: Grimes JM]]
-[[Category: Jones, E Y]]
+[[Category: Harvey DJ]]
-[[Category: Stuart, D I]]
+[[Category: Jones EY]]
-[[Category: Envelope protein]]
+[[Category: Stuart DI]]
-[[Category: Glycoprotein]]
-[[Category: Hemagglutinin]]
-[[Category: Hendra]]
-[[Category: Henipavirus]]
-[[Category: Hev]]
-[[Category: Hev-g]]
-[[Category: Hydrolase]]
-[[Category: Membrane]]
-[[Category: Nipah]]
-[[Category: Niv]]
-[[Category: Niv-g]]
-[[Category: Paramyxovirus]]
-[[Category: Signal-anchor]]
-[[Category: Transmembrane]]
-[[Category: Viral attachment]]
-[[Category: Virion]]
-[[Category: Virus]]

2vwd

From Proteopedia

Current revision

Nipah Virus Attachment Glycoprotein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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