PDBsum entry 2vsm

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
413 a.a. *
137 a.a. *
NAG ×4
Waters ×705
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinb2
Structure: Hemagglutinin-neuraminidase. Chain: a. Fragment: b-propeller, ephrin binding domain, residues 188-602. Synonym: niv-g. Engineered: yes. Other_details: n-acetylglucosamine linkages observed in structure\: asn417 asn529 asn481. Ephrin-b2.
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). Homo sapiens. Human. Organism_taxid: 9606.
1.80Å     R-factor:   0.154     R-free:   0.198
Authors: T.A.Bowden,A.R.Aricescu,R.J.Gilbert,J.M.Grimes,E.Y.Jones, D.I.Stuart
Key ref:
T.A.Bowden et al. (2008). Structural basis of Nipah and Hendra virus attachment to their cell-surface receptor ephrin-B2. Nat Struct Biol, 15, 567-572. PubMed id: 18488039 DOI: 10.1038/nsmb.1435
25-Apr-08     Release date:   20-May-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q9IH62  (GLYCP_NIPAV) -  Glycoprotein G
602 a.a.
413 a.a.
Protein chain
Pfam   ArchSchema ?
P52799  (EFNB2_HUMAN) -  Ephrin-B2
333 a.a.
137 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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


DOI no: 10.1038/nsmb.1435 Nat Struct Biol 15:567-572 (2008)
PubMed id: 18488039  
Structural basis of Nipah and Hendra virus attachment to their cell-surface receptor ephrin-B2.
T.A.Bowden, A.R.Aricescu, R.J.Gilbert, J.M.Grimes, E.Y.Jones, D.I.Stuart.
Nipah and Hendra viruses are emergent paramyxoviruses, causing disease characterized by rapid onset and high mortality rates, resulting in their classification as Biosafety Level 4 pathogens. Their attachment glycoproteins are essential for the recognition of the cell-surface receptors ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3). Here we report crystal structures of both Nipah and Hendra attachment glycoproteins in complex with human EFNB2. In contrast to previously solved paramyxovirus attachment complexes, which are mediated by sialic acid interactions, the Nipah and Hendra complexes are maintained by an extensive protein-protein interface, including a crucial phenylalanine side chain on EFNB2 that fits snugly into a hydrophobic pocket on the viral protein. By analogy with the development of antivirals against sialic acid binding viruses, these results provide a structural template to target antiviral inhibition of protein-protein interactions.
  Selected figure(s)  
Figure 1.
(a) C trace representations of NiV-G- EFNB2 (1.8-Å resolution; NiV-G is blue and EFNB2 is yellow) and HeV-G- EFNB2 (3.3-Å resolution; HeV-G is orange and EFNB2 is cyan) superimposed on the viral receptor component of the complexes. The structures of NiV-G and HeV-G in complex with EFNB2 are practically identical (0.5-Å r.m.s. deviation in equivalent C atoms over residues 189–601). As a result, subsequent figures show the higher-resolution NiV-G- EFNB2 structure, and it will be referred to generically as HNV-G. (b) Cartoon diagram of HNV-G- EFNB2 (colored as a rainbow with the N terminus in blue and the C terminus in red) in complex with EFNB2 ligand (gray). N-acetylglucosamine moieties observed as stubs at the N-linked glycosylation sites in the NiV-G- EFNB2 structure are shown as sticks (pink). (c) Looking down the six-fold -propeller of HNV-G with 2F[o] - F[c] electron density (blue mesh, 1.0 ) and EFNB2 residues 118–126 from the G-H binding loop shown.
Figure 3.
EFNB2 bound to HNV-G is shown as a gray cartoon in stereo. EFNB2 in its apo form (PDB 1IKO; 1.9-Å r.m.s. deviation over 138 equivalent C atoms) is red, EFNB2 bound to EPHB2 (PDB 1NUK; 2.0-Å r.m.s.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2008, 15, 567-572) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21217702 T.Hashiguchi, T.Ose, M.Kubota, N.Maita, J.Kamishikiryo, K.Maenaka, and Y.Yanagi (2011).
Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM.
  Nat Struct Mol Biol, 18, 135-141.
PDB codes: 3alw 3alx 3alz
20010840 C.Santiago, M.L.Celma, T.Stehle, and J.M.Casasnovas (2010).
Structure of the measles virus hemagglutinin bound to the CD46 receptor.
  Nat Struct Mol Biol, 17, 124-129.
PDB code: 3inb
  21073718 D.Khetawat, and C.C.Broder (2010).
A functional henipavirus envelope glycoprotein pseudotyped lentivirus assay system.
  Virol J, 7, 312.  
20519383 H.C.Aguilar, V.Aspericueta, L.R.Robinson, K.E.Aanensen, and B.Lee (2010).
A quantitative and kinetic fusion protein-triggering assay can discern distinct steps in the nipah virus membrane fusion cascade.
  J Virol, 84, 8033-8041.  
19875447 H.Qin, R.Noberini, X.Huan, J.Shi, E.B.Pasquale, and J.Song (2010).
Structural characterization of the EphA4-Ephrin-B2 complex reveals new features enabling Eph-ephrin binding promiscuity.
  J Biol Chem, 285, 644-654.
PDB code: 3gxu
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.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
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
19019819 H.C.Aguilar, Z.A.Ataman, V.Aspericueta, A.Q.Fang, M.Stroud, O.A.Negrete, R.A.Kammerer, and B.Lee (2009).
A Novel Receptor-induced Activation Site in the Nipah Virus Attachment Glycoprotein (G) Involved in Triggering the Fusion Glycoprotein (F).
  J Biol Chem, 284, 1628-1635.  
19216624 P.Prabakaran, Z.Zhu, X.Xiao, A.Biragyn, A.S.Dimitrov, C.C.Broder, and D.S.Dimitrov (2009).
Potent human monoclonal antibodies against SARS CoV, Nipah and Hendra viruses.
  Expert Opin Biol Ther, 9, 355-368.  
  20161127 R.M.Iorio, V.R.Melanson, and P.J.Mahon (2009).
Glycoprotein interactions in paramyxovirus fusion.
  Future Virol, 4, 335-351.  
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
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.  
18523462 B.Lee, Z.A.Ataman, and L.Jin (2008).
Evil versus 'eph-ective' use of ephrin-B2.
  Nat Struct Mol Biol, 15, 540-542.  
19079583 E.Kirchner, K.M.Guglielmi, H.M.Strauss, T.S.Dermody, and T.Stehle (2008).
Structure of reovirus sigma1 in complex with its receptor junctional adhesion molecule-A.
  PLoS Pathog, 4, e1000235.
PDB code: 3eoy
18799571 K.A.Bishop, A.C.Hickey, D.Khetawat, J.R.Patch, K.N.Bossart, Z.Zhu, L.F.Wang, D.S.Dimitrov, and C.C.Broder (2008).
Residues in the stalk domain of the hendra virus g glycoprotein modulate conformational changes associated with receptor binding.
  J Virol, 82, 11398-11409.  
18815311 T.A.Bowden, M.Crispin, D.J.Harvey, A.R.Aricescu, J.M.Grimes, E.Y.Jones, and D.I.Stuart (2008).
Crystal structure and carbohydrate analysis of Nipah virus attachment glycoprotein: a template for antiviral and vaccine design.
  J Virol, 82, 11628-11636.
PDB code: 2vwd
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 codes are shown on the right.