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PDBsum entry 1mql
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Viral protein PDB id
1mql

 

 

 

 

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Contents
Protein chains
318 a.a. *
172 a.a. *
Ligands
NAG ×7
NDG ×12
MAN-MAN
MAN ×4
Waters ×47
* Residue conservation analysis
PDB id:
1mql
Name: Viral protein
Title: Bha of ukr/63
Structure: Hemagglutinin ha1 chain. Chain: a, d, g. Fragment: residues 17-345. Hemagglutinin ha2 chain. Chain: b, e, h. Fragment: residues 346-566
Source: Influenza a virus. Organism_taxid: 11320. Organism_taxid: 11320
Biol. unit: Hexamer (from PQS)
Resolution:
2.90Å     R-factor:   0.269     R-free:   0.306
Authors: Y.Ha,D.J.Stevens,J.J.Skehel,D.C.Wiley
Key ref: Y.Ha et al. (2003). X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus. Virology, 309, 209-218. PubMed id: 12758169 DOI: 10.1016/S0042-6822(03)00068-0
Date:
16-Sep-02     Release date:   26-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03442  (HEMA_I63A3) -  Hemagglutinin from Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
318 a.a.
Protein chains
Pfam   ArchSchema ?
P03442  (HEMA_I63A3) -  Hemagglutinin from Influenza A virus (strain A/Duck/Ukraine/1/1963 H3N8)
Seq:
Struc: 		 
Seq:
Struc: 		566 a.a.
172 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0042-6822(03)00068-0 Virology 309:209-218 (2003)
PubMed id: 12758169  
 
 
X-ray structure of the hemagglutinin of a potential H3 avian progenitor of the 1968 Hong Kong pandemic influenza virus.
Y.Ha, D.J.Stevens, J.J.Skehel, D.C.Wiley.
 
  ABSTRACT  
 
We have determined the structure of the HA of an avian influenza virus, A/duck/Ukraine/63, a member of the same antigenic subtype, H3, as the virus that caused the 1968 Hong Kong influenza pandemic, and a possible progenitor of the pandemic virus. We find that structurally significant differences between the avian and the human HAs are restricted to the receptor-binding site particularly the substitutions Q226L and G228S that cause the site to open and residues within it to rearrange, including the conserved residues Y98, W153, and H183. We have also analyzed complexes formed by the HA with sialopentasaccharides in which the terminal sialic acid is in either alpha2,3- or alpha2,6-linkage to galactose. Comparing the structures of complexes in which an alpha2,3-linked receptor analog is bound to the H3 avian HA or to an H5 avian HA leads to the suggestion that all avian influenza HAs bind to their preferred alpha2,3-linked receptors similarly, with the analog in a trans conformation about the glycosidic linkage. We find that alpha2,6-linked analogs are bound by both human and avian HAs in a cis conformation, and that the incompatibility of an alpha2,6-linked receptor with the alpha2,3-linkage-specific H3 avian HA-binding site is partially resolved by a small change in the position and orientation of the sialic acid. We discuss our results in relation to the mechanism of transfer of influenza viruses between species.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21097900 G.B.Triana-Baltzer, R.L.Sanders, M.Hedlund, K.A.Jensen, L.M.Aschenbrenner, J.L.Larson, and F.Fang (2011).
Phenotypic and genotypic characterization of influenza virus mutants selected with the sialidase fusion protein DAS181.
  J Antimicrob Chemother, 66, 15-28.  
21251008 T.Han, and W.A.Marasco (2011).
Structural basis of influenza virus neutralization.
  Ann N Y Acad Sci, 1217, 178-190.  
20734133 K.Viswanathan, A.Chandrasekaran, A.Srinivasan, R.Raman, V.Sasisekharan, and R.Sasisekharan (2010).
Glycans as receptors for influenza pathogenesis.
  Glycoconj J, 27, 561-570.  
19856192 M.N.Al-qattan, and M.N.Mordi (2010).
Site-directed fragment-based generation of virtual sialic acid databases against influenza A hemagglutinin.
  J Mol Model, 16, 975-991.  
19906932 R.L.Graham, and R.S.Baric (2010).
Recombination, reservoirs, and the modular spike: mechanisms of coronavirus cross-species transmission.
  J Virol, 84, 3134-3146.  
20007271 R.Xu, R.McBride, J.C.Paulson, C.F.Basler, and I.A.Wilson (2010).
Structure, receptor binding, and antigenicity of influenza virus hemagglutinins from the 1957 H2N2 pandemic.
  J Virol, 84, 1715-1721.
PDB codes: 3ku3 3ku5 3ku6
20538598 S.J.Gamblin, and J.J.Skehel (2010).
Influenza hemagglutinin and neuraminidase membrane glycoproteins.
  J Biol Chem, 285, 28403-28409.  
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.  
19356594 D.Xu, E.I.Newhouse, R.E.Amaro, H.C.Pao, L.S.Cheng, P.R.Markwick, J.A.McCammon, W.W.Li, and P.W.Arzberger (2009).
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective.
  J Mol Biol, 387, 465-491.  
19891427 E.I.Newhouse, D.Xu, P.R.Markwick, R.E.Amaro, H.C.Pao, K.J.Wu, M.Alam, J.A.McCammon, and W.W.Li (2009).
Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective.
  J Am Chem Soc, 131, 17430-17442.  
19805083 J.Liu, D.J.Stevens, L.F.Haire, P.A.Walker, P.J.Coombs, R.J.Russell, S.J.Gamblin, and J.J.Skehel (2009).
Structures of receptor complexes formed by hemagglutinins from the Asian Influenza pandemic of 1957.
  Proc Natl Acad Sci U S A, 106, 17175-17180.
PDB codes: 2wr0 2wr1 2wr2 2wr3 2wr4 2wr5 2wr7 2wrb 2wrc 2wrd 2wre 2wrf 2wrg 2wrh
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
19458903 J.Uhlendorff, T.Matrosovich, H.D.Klenk, and M.Matrosovich (2009).
Functional significance of the hemadsorption activity of influenza virus neuraminidase and its alteration in pandemic viruses.
  Arch Virol, 154, 945-957.  
19193808 M.L.Reed, H.L.Yen, R.M.DuBois, O.A.Bridges, R.Salomon, R.G.Webster, and C.J.Russell (2009).
Amino acid residues in the fusion peptide pocket regulate the pH of activation of the H5N1 influenza virus hemagglutinin protein.
  J Virol, 83, 3568-3580.  
19300497 R.Yoshida, M.Igarashi, H.Ozaki, N.Kishida, D.Tomabechi, H.Kida, K.Ito, and A.Takada (2009).
Cross-protective potential of a novel monoclonal antibody directed against antigenic site B of the hemagglutinin of influenza A viruses.
  PLoS Pathog, 5, e1000350.  
19157478 U.Neu, T.Stehle, and W.J.Atwood (2009).
The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry.
  Virology, 384, 389-399.  
19706746 Z.Xia, G.Jin, J.Zhu, and R.Zhou (2009).
Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.
  Bioinformatics, 25, 2309-2317.  
18176555 A.Chandrasekaran, A.Srinivasan, R.Raman, K.Viswanathan, S.Raguram, T.M.Tumpey, V.Sasisekharan, and R.Sasisekharan (2008).
Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin.
  Nat Biotechnol, 26, 107-113.  
  18652681 A.S.Gambaryan, A.B.Tuzikov, G.V.Pazynina, J.A.Desheva, N.V.Bovin, M.N.Matrosovich, and A.I.Klimov (2008).
6-sulfo sialyl Lewis X is the common receptor determinant recognized by H5, H6, H7 and H9 influenza viruses of terrestrial poultry.
  Virol J, 5, 85.  
18451985 B.P.Blackburne, A.J.Hay, and R.A.Goldstein (2008).
Changing selective pressure during antigenic changes in human influenza H3.
  PLoS Pathog, 4, e1000058.  
18772285 C.R.Parrish, E.C.Holmes, D.M.Morens, E.C.Park, D.S.Burke, C.H.Calisher, C.A.Laughlin, L.J.Saif, and P.Daszak (2008).
Cross-species virus transmission and the emergence of new epidemic diseases.
  Microbiol Mol Biol Rev, 72, 457-470.  
18829764 L.Keleta, A.Ibricevic, N.V.Bovin, S.L.Brody, and E.G.Brown (2008).
Experimental evolution of human influenza virus H3 hemagglutinin in the mouse lung identifies adaptive regions in HA1 and HA2.
  J Virol, 82, 11599-11608.  
18574690 T.Sawada, T.Hashimoto, H.Tokiwa, T.Suzuki, H.Nakano, H.Ishida, M.Kiso, and Y.Suzuki (2008).
Ab initio fragment molecular orbital studies of influenza virus hemagglutinin-sialosaccharide complexes toward chemical clarification about the virus host range determination.
  Glycoconj J, 25, 805-815.  
  19565017 T.Sawada, T.Hashimoto, H.Tokiwa, T.Suzuki, H.Nakano, H.Ishida, M.Kiso, and Y.Suzuki (2008).
Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors.
  J Mol Genet Med, 3, 133-142.  
17942670 Q.Wang, X.Tian, X.Chen, and J.Ma (2007).
Structural basis for receptor specificity of influenza B virus hemagglutinin.
  Proc Natl Acad Sci U S A, 104, 16874-16879.
PDB codes: 2rft 2rfu
16575526 L.Glaser, D.Zamarin, H.M.Acland, E.Spackman, P.Palese, A.García-Sastre, and D.Tewari (2006).
Sequence analysis and receptor specificity of the hemagglutinin of a recent influenza H2N2 virus isolated from chicken in North America.
  Glycoconj J, 23, 93-99.  
16575525 R.J.Russell, D.J.Stevens, L.F.Haire, S.J.Gamblin, and J.J.Skehel (2006).
Avian and human receptor binding by hemagglutinins of influenza A viruses.
  Glycoconj J, 23, 85-92.  
16153179 C.R.Parrish, and Y.Kawaoka (2005).
The origins of new pandemic viruses: the acquisition of new host ranges by canine parvovirus and influenza A viruses.
  Annu Rev Microbiol, 59, 553-586.  
14671130 R.Harvey, A.C.Martin, M.Zambon, and W.S.Barclay (2004).
Restrictions to the adaptation of influenza a virus h5 hemagglutinin to the human host.
  J Virol, 78, 502-507.  
14764886 S.J.Gamblin, L.F.Haire, R.J.Russell, D.J.Stevens, B.Xiao, Y.Ha, N.Vasisht, D.A.Steinhauer, R.S.Daniels, A.Elliot, D.C.Wiley, and J.J.Skehel (2004).
The structure and receptor binding properties of the 1918 influenza hemagglutinin.
  Science, 303, 1838-1842.
PDB codes: 1ru7 1ruy 1ruz 1rv0 1rvt 1rvx 1rvz
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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