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PDBsum entry 2vwd

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2vwd
Jmol
Contents
Protein chains
413 a.a. *
Ligands
GBL ×8
NAG ×10
Metals
_CL ×2
Waters ×578
* Residue conservation analysis
PDB id:
2vwd
Name: Hydrolase
Title: Nipah virus attachment glycoprotein
Structure: Hemagglutinin-neuraminidase. Chain: a, b. Fragment: receptor-binding domain, residues 183-602. Synonym: niv-g. Engineered: yes
Source: Nipah virus. Organism_taxid: 121791. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: human embryonic kidney 293t. Other_details: synthetically optimized cdna (geneart)
Resolution:
2.25Å     R-factor:   0.175     R-free:   0.221
Authors: T.A.Bowden,M.Crispin,D.J.Harvey,A.R.Aricescu,J.M.Grimes,E.Y. D.I.Stuart
Key ref: T.A.Bowden et al. (2008). Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design. J Virol, 82, 11628-11636. PubMed id: 18815311
Date:
20-Jun-08     Release date:   07-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9IH62  (GLYCP_NIPAV) -  Glycoprotein G
Seq:
Struc:
 
Seq:
Struc:
602 a.a.
413 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   1 term 
  Biological process     viral infectious cycle   1 term 
  Biochemical function     host cell surface receptor binding     2 terms  

 

 
J Virol 82:11628-11636 (2008)
PubMed id: 18815311  
 
 
Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design.
T.A.Bowden, M.Crispin, D.J.Harvey, A.R.Aricescu, J.M.Grimes, E.Y.Jones, D.I.Stuart.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472575 D.J.Harvey, F.Sobott, M.Crispin, A.Wrobel, C.Bonomelli, S.Vasiljevic, C.N.Scanlan, C.A.Scarff, K.Thalassinos, and J.H.Scrivens (2011).
Ion mobility mass spectrometry for extracting spectra of N-glycans directly from incubation mixtures following glycan release: application to glycans from engineered glycoforms of intact, folded HIV gp120.
  J Am Soc Mass Spectrom, 22, 568-581.  
20181792 D.C.Dunlop, C.Bonomelli, F.Mansab, S.Vasiljevic, K.J.Doores, M.R.Wormald, A.S.Palma, T.Feizi, D.J.Harvey, R.A.Dwek, M.Crispin, and C.N.Scanlan (2010).
Polysaccharide mimicry of the epitope of the broadly neutralizing anti-HIV antibody, 2G12, induces enhanced antibody responses to self oligomannose glycans.
  Glycobiology, 20, 812-823.  
20657787 J.Habchi, L.Mamelli, H.Darbon, and S.Longhi (2010).
Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment.
  PLoS One, 5, e11684.  
20375167 T.A.Bowden, M.Crispin, D.J.Harvey, E.Y.Jones, and D.I.Stuart (2010).
Dimeric architecture of the Hendra virus attachment glycoprotein: evidence for a conserved mode of assembly.
  J Virol, 84, 6208-6217.
PDB code: 2x9m
19710150 S.A.Connolly, G.P.Leser, T.S.Jardetzky, and R.A.Lamb (2009).
Bimolecular complementation of paramyxovirus fusion and hemagglutinin-neuraminidase proteins enhances fusion: implications for the mechanism of fusion triggering.
  J Virol, 83, 10857-10868.  
19836338 T.A.Bowden, A.R.Aricescu, J.E.Nettleship, C.Siebold, N.Rahman-Huq, R.J.Owens, D.I.Stuart, and E.Y.Jones (2009).
Structural plasticity of eph receptor A4 facilitates cross-class ephrin signaling.
  Structure, 17, 1386-1397.
PDB codes: 2wo1 2wo2 2wo3
19494008 T.A.Bowden, M.Crispin, S.C.Graham, D.J.Harvey, J.M.Grimes, E.Y.Jones, and D.I.Stuart (2009).
Unusual molecular architecture of the machupo virus attachment glycoprotein.
  J Virol, 83, 8259-8265.
PDB code: 2wfo
19656895 T.Paal, M.A.Brindley, C.St Clair, A.Prussia, D.Gaus, S.A.Krumm, J.P.Snyder, and R.K.Plemper (2009).
Probing the spatial organization of measles virus fusion complexes.
  J Virol, 83, 10480-10493.  
19342221 T.Stehle, and J.M.Casasnovas (2009).
Specificity switching in virus-receptor complexes.
  Curr Opin Struct Biol, 19, 181-188.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.