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PDBsum entry 1ken
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protein ligands Protein-protein interface(s) links
Viral protein/immune system PDB id
1ken

 

 

 

 

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Contents
Protein chains
320 a.a. *
175 a.a. *
213 a.a. *
221 a.a. *
Ligands
NAG-NAG-MAN ×3
* Residue conservation analysis
PDB id:
1ken
Name: Viral protein/immune system
Title: Influenza virus hemagglutinin complexed with an antibody that prevents the hemagglutinin low ph fusogenic transition
Structure: Hemagglutinin ha1. Chain: a, c, e. Hemagglutinin ha2. Chain: b, d, f. Fragment: fab fragment of antibody. Other_details: bromelain digested. Influenza virus infectivity neutralizing antibody (light chain). Chain: l, u.
Source: Influenza a virus (a/x-31(h3n2)). Organism_taxid: 132504. Strain: x31. Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Decamer (from PQS)
Resolution:
3.50Å     R-factor:   0.255     R-free:   0.323
Authors: C.Barbey-Martin,B.Gigant,T.Bizebard,L.J.Calder,S.A.Wharto,J.J.Skehel, M.Knossow
Key ref: C.Barbey-Martin et al. (2002). An antibody that prevents the hemagglutinin low pH fusogenic transition. Virology, 294, 70-74. PubMed id: 11886266
Date:
16-Nov-01     Release date:   24-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03438  (HEMA_I000X) -  Hemagglutinin from Influenza A virus (strain A/X-31 H3N2)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
320 a.a.*
Protein chains
Pfam   ArchSchema ?
P03437  (HEMA_I68A0) -  Hemagglutinin from Influenza A virus (strain A/Aichi/2/1968 H3N2)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
175 a.a.
Protein chains
Pfam   ArchSchema ?
P01837  (IGKC_MOUSE) -  Immunoglobulin kappa constant from Mus musculus
Seq:
Struc: 		107 a.a.
213 a.a.*
Protein chains
Pfam   ArchSchema ?
P01869  (IGH1M_MOUSE) -  Ig gamma-1 chain C region, membrane-bound form from Mus musculus
Seq:
Struc: 		393 a.a.
221 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 

 
Virology 294:70-74 (2002)
PubMed id: 11886266  
 
 
An antibody that prevents the hemagglutinin low pH fusogenic transition.
C.Barbey-Martin, B.Gigant, T.Bizebard, L.J.Calder, S.A.Wharton, J.J.Skehel, M.Knossow.
 
  ABSTRACT  
 
We have determined the structure of a complex of influenza hemagglutinin (HA) with an antibody that binds simultaneously to the membrane-distal domains of two HA monomers, effectively cross-linking them. The antibody prevents the low pH structural transition of HA that is required for its membrane fusion activity, providing evidence that a rearrangement of HA membrane-distal domains is an essential component of the transition.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22982990 D.C.Ekiert, A.K.Kashyap, J.Steel, A.Rubrum, G.Bhabha, R.Khayat, J.H.Lee, M.A.Dillon, R.E.O'Neil, A.M.Faynboym, M.Horowitz, L.Horowitz, A.B.Ward, P.Palese, R.Webby, R.A.Lerner, R.R.Bhatt, and I.A.Wilson (2012).
Cross-neutralization of influenza A viruses mediated by a single antibody loop.
  Nature, 489, 526-532.
PDB codes: 4fnk 4fnl 4fp8 4fqr
21342562 J.W.Huang, and J.M.Yang (2011).
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses.
  BMC Bioinformatics, 12, S31.  
21251008 T.Han, and W.A.Marasco (2011).
Structural basis of influenza virus neutralization.
  Ann N Y Acad Sci, 1217, 178-190.  
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
19381281 H.L.Yen, and J.S.Peiris (2009).
Mapping antibody epitopes of the avian H5N1 influenza virus.
  PLoS Med, 6, e1000064.  
  20025194 J.L.Cherry, D.J.Lipman, A.Nikolskaya, and Y.I.Wolf (2009).
Evolutionary dynamics of N-glycosylation sites of influenza virus hemagglutinin.
  PLoS Curr, 1, RRN1001.  
19031453 J.Shen, B.D.Kirk, J.Ma, and Q.Wang (2009).
Diversifying selective pressure on influenza B virus hemagglutinin.
  J Med Virol, 81, 114-124.  
19234466 J.Sui, W.C.Hwang, S.Perez, G.Wei, D.Aird, L.M.Chen, E.Santelli, B.Stec, G.Cadwell, M.Ali, H.Wan, A.Murakami, A.Yammanuru, T.Han, N.J.Cox, L.A.Bankston, R.O.Donis, R.C.Liddington, and W.A.Marasco (2009).
Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses.
  Nat Struct Mol Biol, 16, 265-273.
PDB code: 3fku
19079256 M.F.Delgado, S.Coviello, A.C.Monsalvo, G.A.Melendi, J.Z.Hernandez, J.P.Batalle, L.Diaz, A.Trento, H.Y.Chang, W.Mitzner, J.Ravetch, J.A.Melero, P.M.Irusta, and F.P.Polack (2009).
Lack of antibody affinity maturation due to poor Toll-like receptor stimulation leads to enhanced respiratory syncytial virus disease.
  Nat Med, 15, 34-41.  
19452551 N.Kowalsman, and M.Eisenstein (2009).
Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models.
  Proteins, 77, 297-318.  
19234464 T.T.Wang, and P.Palese (2009).
Universal epitopes of influenza virus hemagglutinins?
  Nat Struct Mol Biol, 16, 233-234.  
18197170 G.B.Karlsson Hedestam, R.A.Fouchier, S.Phogat, D.R.Burton, J.Sodroski, and R.T.Wyatt (2008).
The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus.
  Nat Rev Microbiol, 6, 143-155.  
18824612 G.Conti, W.Magliani, S.Conti, L.Nencioni, R.Sgarbanti, A.T.Palamara, and L.Polonelli (2008).
Therapeutic activity of an anti-idiotypic antibody-derived killer peptide against influenza A virus experimental infection.
  Antimicrob Agents Chemother, 52, 4331-4337.  
18184701 Q.Wang, F.Cheng, M.Lu, X.Tian, and J.Ma (2008).
Crystal structure of unliganded influenza B virus hemagglutinin.
  J Virol, 82, 3011-3020.
PDB code: 3bt6
16925526 M.Knossow, and J.J.Skehel (2006).
Variation and infectivity neutralization in influenza.
  Immunology, 119, 1-7.  
15981246 D.Law, M.Hotchko, and L.Ten Eyck (2005).
Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes.
  Proteins, 60, 302-307.  
15956598 J.B.Pesavento, S.E.Crawford, E.Roberts, M.K.Estes, and B.V.Prasad (2005).
pH-induced conformational change of the rotavirus VP4 spike: implications for cell entry and antibody neutralization.
  J Virol, 79, 8572-8580.  
15659362 J.Janin (2005).
Assessing predictions of protein-protein interaction: the CAPRI experiment.
  Protein Sci, 14, 278-283.  
12784373 C.J.Camacho, and D.W.Gatchell (2003).
Successful discrimination of protein interactions.
  Proteins, 52, 92-97.  
12784374 D.W.Ritchie (2003).
Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2.
  Proteins, 52, 98.  
12784366 E.Ben-Zeev, A.Berchanski, A.Heifetz, B.Shapira, and M.Eisenstein (2003).
Prediction of the unknown: inspiring experience with the CAPRI experiment.
  Proteins, 52, 41-46.  
12784370 G.R.Smith, and M.J.Sternberg (2003).
Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial.
  Proteins, 52, 74-79.  
12784376 J.Fernández-Recio, M.Totrov, and R.Abagyan (2003).
ICM-DISCO docking by global energy optimization with fully flexible side-chains.
  Proteins, 52, 113-117.  
12831891 J.Janin, and B.Séraphin (2003).
Genome-wide studies of protein-protein interaction.
  Curr Opin Struct Biol, 13, 383-388.  
12784359 J.Janin, K.Henrick, J.Moult, L.T.Eyck, M.J.Sternberg, S.Vajda, I.Vakser, and S.J.Wodak (2003).
CAPRI: a Critical Assessment of PRedicted Interactions.
  Proteins, 52, 2-9.  
12784369 R.Chen, W.Tong, J.Mintseris, L.Li, and Z.Weng (2003).
ZDOCK predictions for the CAPRI challenge.
  Proteins, 52, 68-73.  
12784368 R.Méndez, R.Leplae, L.De Maria, and S.J.Wodak (2003).
Assessment of blind predictions of protein-protein interactions: current status of docking methods.
  Proteins, 52, 51-67.  
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.

 

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