PDBsum entry 2vir

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protein metals Protein-protein interface(s) links
Complex (hemagglutinin/immmunoglobulin) PDB id
Protein chains
210 a.a. *
221 a.a. *
267 a.a. *
_ZN ×3
* Residue conservation analysis
PDB id:
Name: Complex (hemagglutinin/immmunoglobulin)
Title: Influenza virus hemagglutinin complexed with a neutralizing antibody
Structure: Immunoglobulin (igg1, lambda). Chain: a. Fragment: fab fragment. Immunoglobulin (igg1, lambda). Chain: b. Fragment: fab fragment. Hemagglutinin. Chain: c. Fragment: proteolytic fragment "ha top" containing ha1
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Cell: hybridoma. Strain: balb-c. Influenza a virus (a/x-31(h3n2)). Organism_taxid: 132504. Strain: x31.
Biol. unit: Homo-Trimer (from PDB file)
3.25Å     R-factor:   0.198     R-free:   0.249
Authors: T.Bizebard,D.Fleury,B.Gigant,S.A.Wharton,J.J.Skehel, M.Knossow
Key ref: D.Fleury et al. (1998). Antigen distortion allows influenza virus to escape neutralization. Nat Struct Biol, 5, 119-123. PubMed id: 9461077
22-Dec-97     Release date:   29-Apr-98    
Supersedes: 1vir
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Protein chain
No UniProt id for this chain
Struc: 210 a.a.
Protein chain
Pfam   ArchSchema ?
Q99LC4  (Q99LC4_MOUSE) -  Igh protein
463 a.a.
221 a.a.*
Protein chain
Pfam   ArchSchema ?
P03437  (HEMA_I68A0) -  Hemagglutinin
566 a.a.
267 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 71 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   1 term 
  Biological process     viral envelope fusion with host membrane   1 term 
  Biochemical function     host cell surface receptor binding     1 term  


Nat Struct Biol 5:119-123 (1998)
PubMed id: 9461077  
Antigen distortion allows influenza virus to escape neutralization.
D.Fleury, S.A.Wharton, J.J.Skehel, M.Knossow, T.Bizebard.
The structure of the hemagglutinin (HA) of a mutant influenza virus that escapes neutralization by a monoclonal antibody shows that the mutation causes changes in HA structure which avoid an energetically less favorable conformation. However, the structure of the mutant HA.Fab complex indicates that the antibody binds selectively to mutant HA in a wild type-like distorted conformation. The association of an antibody with a less favored HA conformation represents an alternative to previously described mechanisms of escape from neutralization by antibodies.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21213247 P.L.Kastritis, I.H.Moal, H.Hwang, Z.Weng, P.A.Bates, A.M.Bonvin, and J.Janin (2011).
A structure-based benchmark for protein-protein binding affinity.
  Protein Sci, 20, 482-491.  
21251008 T.Han, and W.A.Marasco (2011).
Structural basis of influenza virus neutralization.
  Ann N Y Acad Sci, 1217, 178-190.  
20232097 A.Malik, A.Firoz, V.Jha, E.Sunderasan, and S.Ahmad (2010).
Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin.
  J Mol Model, 16, 1883-1893.  
20038580 A.Yokota, K.Tsumoto, M.Shiroishi, T.Nakanishi, H.Kondo, and I.Kumagai (2010).
Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme.
  J Biol Chem, 285, 7686-7696.
PDB codes: 3a67 3a6b 3a6c
20388627 W.D.Lees, D.S.Moss, and A.J.Shepherd (2010).
A computational analysis of the antigenic properties of haemagglutinin in influenza A H3N2.
  Bioinformatics, 26, 1403-1408.  
20602265 Y.Sun, Y.Shi, W.Zhang, Q.Li, D.Liu, C.Vavricka, J.Yan, and G.F.Gao (2010).
In silico characterization of the functional and structural modules of the hemagglutinin protein from the swine-origin influenza virus A (H1N1)-2009.
  Sci China Life Sci, 53, 633-642.  
19251591 D.C.Ekiert, G.Bhabha, M.A.Elsliger, R.H.Friesen, M.Jongeneelen, M.Throsby, J.Goudsmit, and I.A.Wilson (2009).
Antibody recognition of a highly conserved influenza virus epitope.
  Science, 324, 246-251.
PDB codes: 3gbm 3gbn
17996091 B.D.Silverman (2007).
Using molecular principal axes for structural comparison: determining the tertiary changes of a FAB antibody domain induced by antigenic binding.
  BMC Struct Biol, 7, 77.  
17166830 M.Shiroishi, K.Tsumoto, Y.Tanaka, A.Yokota, T.Nakanishi, H.Kondo, and I.Kumagai (2007).
Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL.
  J Biol Chem, 282, 6783-6791.
PDB codes: 2dqc 2dqd 2dqe 2dqf 2dqg 2dqh 2dqi 2dqj
17040574 B.J.Hanson, A.C.Boon, A.P.Lim, A.Webb, E.E.Ooi, and R.J.Webby (2006).
Passive immunoprophylaxis and therapy with humanized monoclonal antibody specific for influenza A H5 hemagglutinin in mice.
  Respir Res, 7, 126.  
16925526 M.Knossow, and J.J.Skehel (2006).
Variation and infectivity neutralization in influenza.
  Immunology, 119, 1-7.  
16252003 J.Yan, W.Wen, W.Xu, J.F.Long, M.E.Adams, S.C.Froehner, and M.Zhang (2005).
Structure of the split PH domain and distinct lipid-binding properties of the PH-PDZ supramodule of alpha-syntrophin.
  EMBO J, 24, 3985-3995.
PDB codes: 1z86 1z87 2adz
15858030 K.Nakajima, E.Nobusawa, A.Nagy, and S.Nakajima (2005).
Accumulation of amino acid substitutions promotes irreversible structural changes in the hemagglutinin of human influenza AH3 virus during evolution.
  J Virol, 79, 6472-6477.  
12709438 I.Kumagai, Y.Nishimiya, H.Kondo, and K.Tsumoto (2003).
Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10.
  J Biol Chem, 278, 24929-24936.
PDB codes: 1ua6 1uac
11517321 I.B.Rasmussen, E.Lunde, T.E.Michaelsen, B.Bogen, and I.Sandlie (2001).
The principle of delivery of T cell epitopes to antigen-presenting cells applied to peptides from influenza virus, ovalbumin, and hen egg lysozyme: implications for peptide vaccination.
  Proc Natl Acad Sci U S A, 98, 10296-10301.  
10899782 D.Fleury, R.S.Daniels, J.J.Skehel, M.Knossow, and T.Bizebard (2000).
Structural evidence for recognition of a single epitope by two distinct antibodies.
  Proteins, 40, 572-578.
PDB code: 1eo8
10966468 J.J.Skehel, and D.C.Wiley (2000).
Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin.
  Annu Rev Biochem, 69, 531-569.  
10451557 B.Selisko, A.F.Licea, B.Becerril, F.Zamudio, L.D.Possani, and E.Horjales (1999).
Antibody BCF2 against scorpion toxin Cn2 from Centuroides noxius Hoffmann: primary structure and three-dimensional model as free Fv fragment and complexed with its antigen.
  Proteins, 37, 130-143.  
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.