PDBsum entry 1ruz

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Viral protein PDB id
Protein chains
324 a.a. *
160 a.a. *
NDG ×9
NAG ×2
Waters ×549
* Residue conservation analysis
PDB id:
Name: Viral protein
Title: 1918 h1 hemagglutinin
Structure: Hemagglutinin. Chain: h, j, l. Other_details: hemagglutinin ha1 chain. Hemagglutinin. Chain: i, k, m. Other_details: hemagglutinin ha2 chain
Source: Influenza a virus (a/south carolina/1/ (h1n1)). Organism_taxid: 59375. Strain: a-south carolina-1-18 (h1n1). Cell: vaccinia virus infected cv1 cells. Cell: vaccinia virus infected cv1 cells
Biol. unit: Hexamer (from PQS)
2.90Å     R-factor:   0.248     R-free:   0.289
Authors: J.J.Skehel,S.J.Gamblin,L.F.Haire,R.J.Russell,D.J.Stevens,B.X N.Vasisht,D.A.Steinhauer,R.S.Daniels
Key ref:
S.J.Gamblin et al. (2004). The structure and receptor binding properties of the 1918 influenza hemagglutinin. Science, 303, 1838-1842. PubMed id: 14764886 DOI: 10.1126/science.1093155
12-Dec-03     Release date:   30-Mar-04    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q9WFX3  (HEMA_I18A0) -  Hemagglutinin
566 a.a.
324 a.a.*
Protein chains
Pfam   ArchSchema ?
Q9WFX3  (HEMA_I18A0) -  Hemagglutinin
566 a.a.
160 a.a.
Key:    PfamA 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   1 term 
  Biological process     viral envelope fusion with host membrane   1 term 
  Biochemical function     host cell surface receptor binding     1 term  


DOI no: 10.1126/science.1093155 Science 303:1838-1842 (2004)
PubMed id: 14764886  
The structure and receptor binding properties of the 1918 influenza hemagglutinin.
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, J.J.Skehel.
The 1918 influenza pandemic resulted in about 20 million deaths. This enormous impact, coupled with renewed interest in emerging infections, makes characterization of the virus involved a priority. Receptor binding, the initial event in virus infection, is a major determinant of virus transmissibility that, for influenza viruses, is mediated by the hemagglutinin (HA) membrane glycoprotein. We have determined the crystal structures of the HA from the 1918 virus and two closely related HAs in complex with receptor analogs. They explain how the 1918 HA, while retaining receptor binding site amino acids characteristic of an avian precursor HA, is able to bind human receptors and how, as a consequence, the virus was able to spread in the human population.
  Selected figure(s)  
Figure 1.
Fig. 1. Sequence alignment of 1918-human, 1930-swine, and 1934-human HAs. The subdomain structure of HA in the two polypeptides, HA1 and HA2, that form each monomer is indicated by the colored bars above the sequences. Carbohydrate attachment sites are shaded gray. Residue numbering is on the basis of H3 HA sequence (1). Nonconserved residues are in red.
Figure 5.
Fig. 5. Superposition of the binding site of 1934-human HA in its uncomplexed state and complexed with avian receptor analog. The HA is shown in green in both cases, and the avian receptor is colored as in Fig. 3. Two water molecules, shown as green spheres, link Glu190 to Gln226 in the avian receptor complex. This hydrogen-bonded network is not formed in the uncomplexed structure or in the human receptor complex not shown.
  The above figures are reprinted by permission from the AAAs: Science (2004, 303, 1838-1842) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21106732 H.Shelton, G.Ayora-Talavera, J.Ren, S.Loureiro, R.J.Pickles, W.S.Barclay, and I.M.Jones (2011).
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20824086 H.Yang, L.M.Chen, P.J.Carney, R.O.Donis, and J.Stevens (2010).
Structures of receptor complexes of a North American H7N2 influenza hemagglutinin with a loop deletion in the receptor binding site.
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PDB codes: 3m5g 3m5h 3m5i 3m5j
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Monoclonal antibodies specific for discontinuous epitopes direct refolding of influenza A virus hemagglutinin.
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20428231 M.Kuroda, H.Katano, N.Nakajima, M.Tobiume, A.Ainai, T.Sekizuka, H.Hasegawa, M.Tashiro, Y.Sasaki, Y.Arakawa, S.Hata, M.Watanabe, and T.Sata (2010).
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20113569 N.A.Ilyushina, J.K.Kim, N.J.Negovetich, Y.K.Choi, V.Lang, N.V.Bovin, H.L.Forrest, M.S.Song, P.N.Pascua, C.J.Kim, R.G.Webster, and R.J.Webby (2010).
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20007353 N.Takemae, R.Ruttanapumma, S.Parchariyanon, S.Yoneyama, T.Hayashi, H.Hiramatsu, N.Sriwilaijaroen, Y.Uchida, S.Kondo, H.Yagi, K.Kato, Y.Suzuki, and T.Saito (2010).
Alterations in receptor-binding properties of swine influenza viruses of the H1 subtype after isolation in embryonated chicken eggs.
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  20630098 P.Suphaphiphat, M.Franti, A.Hekele, A.Lilja, T.Spencer, E.Settembre, G.Palmer, S.Crotta, A.B.Tuccino, B.Keiner, H.Trusheim, K.Balabanis, M.Sackal, M.Rothfeder, C.W.Mandl, P.R.Dormitzer, and P.W.Mason (2010).
Mutations at positions 186 and 194 in the HA gene of the 2009 H1N1 pandemic influenza virus improve replication in cell culture and eggs.
  Virol J, 7, 157.  
20339031 R.Xu, D.C.Ekiert, J.C.Krause, R.Hai, J.E.Crowe, and I.A.Wilson (2010).
Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus.
  Science, 328, 357-360.
PDB codes: 3lzf 3lzg
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.  
20059763 T.Reichert, G.Chowell, H.Nishiura, R.A.Christensen, and J.A.McCullers (2010).
Does Glycosylation as a modifier of Original Antigenic Sin explain the case age distribution and unusual toxicity in pandemic novel H1N1 influenza?
  BMC Infect Dis, 10, 5.  
20809098 X.Ding, L.Jiang, C.Ke, Z.Yang, C.Lei, K.Cao, J.Xu, L.Xu, X.Yang, Y.Zhang, P.Huang, W.Huang, X.Zhu, Z.He, L.Liu, J.Li, J.Yuan, J.Wu, X.Tang, and M.Li (2010).
Amino acid sequence analysis and identification of mutations under positive selection in hemagglutinin of 2009 influenza A (H1N1) isolates.
  Virus Genes, 41, 329-340.  
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
  20948674 D.M.Tscherne, and A.García-Sastre (2009).
Recent strategies to identify broadly neutralizing antibodies against influenza A virus.
  F1000 Biol Rep, 1, 0.  
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.  
  19493338 G.K.Goh, A.K.Dunker, and V.N.Uversky (2009).
Protein intrinsic disorder and influenza virulence: the 1918 H1N1 and H5N1 viruses.
  Virol J, 6, 69.  
20016966 H.Zhang (2009).
Tissue and host tropism of influenza viruses: importance of quantitative analysis.
  Sci China C Life Sci, 52, 1101-1110.  
19381264 J.D.Bloom, and M.J.Glassman (2009).
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin.
  PLoS Comput Biol, 5, e1000349.  
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
19924230 J.Shen, J.Ma, and Q.Wang (2009).
Evolutionary trends of A(H1N1) influenza virus hemagglutinin since 1918.
  PLoS One, 4, e7789.  
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
18785239 K.M.Downard, B.Morrissey, and A.B.Schwahn (2009).
Mass spectrometry analysis of the influenza virus.
  Mass Spectrom Rev, 28, 35-49.  
19421326 L.Sun, X.Lu, C.Li, M.Wang, Q.Liu, Z.Li, X.Hu, J.Li, F.Liu, Q.Li, J.A.Belser, K.Hancock, Y.Shu, J.M.Katz, M.Liang, and D.Li (2009).
Generation, characterization and epitope mapping of two neutralizing and protective human recombinant antibodies against influenza A H5N1 viruses.
  PLoS ONE, 4, e5476.  
19517011 M.Iqbal, T.Yaqub, K.Reddy, and J.W.McCauley (2009).
Novel genotypes of H9N2 influenza A viruses isolated from poultry in Pakistan containing NS genes similar to highly pathogenic H7N3 and H5N1 viruses.
  PLoS One, 4, e5788.  
19056784 M.L.DeMarco, and R.J.Woods (2009).
Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside-protein recognition at membrane surfaces.
  Glycobiology, 19, 344-355.  
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.  
19958488 N.Jongkon, W.Mokmak, D.Chuakheaw, P.J.Shaw, S.Tongsima, and C.Sangma (2009).
Prediction of avian influenza A binding preference to human receptor using conformational analysis of receptor bound to hemagglutinin.
  BMC Genomics, 10, S24.  
19241254 O.Martinez, T.Tsibane, and C.F.Basler (2009).
Neutralizing anti-influenza virus monoclonal antibodies: therapeutics and tools for discovery.
  Int Rev Immunol, 28, 69-92.  
19930664 P.C.Reading, D.L.Pickett, M.D.Tate, P.G.Whitney, E.R.Job, and A.G.Brooks (2009).
Loss of a single N-linked glycan from the hemagglutinin of influenza virus is associated with resistance to collectins and increased virulence in mice.
  Respir Res, 10, 117.  
19399777 P.Das, J.Li, A.K.Royyuru, and R.Zhou (2009).
Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity.
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19637916 P.M.Kasson, D.L.Ensign, and V.S.Pande (2009).
Combining molecular dynamics with bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin.
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18618705 Q.Huang, T.Korte, P.S.Rachakonda, E.W.Knapp, and A.Herrmann (2009).
Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits.
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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.
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Coming soon to an ICU near you: severe pandemic influenza in ICU patients in Spain.
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Hydrogen bond driven self-assembled C2-symmetric chlorin syn dimers; unorthodox models for chlorophyll 'special pairs' in photosynthetic reaction centres.
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The Polyomaviridae: Contributions of virus structure to our understanding of virus receptors and infectious entry.
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Extrapolating from sequence--the 2009 H1N1 'swine' influenza virus.
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Using a mutual information-based site transition network to map the genetic evolution of influenza A/H3N2 virus.
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18176555 A.Chandrasekaran, A.Srinivasan, R.Raman, K.Viswanathan, S.Raguram, T.M.Tumpey, V.Sasisekharan, and R.Sasisekharan (2008).
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Crystal structure of unliganded influenza B virus hemagglutinin.
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PDB code: 3bt6
17936324 S.Thoennes, Z.N.Li, B.J.Lee, W.A.Langley, J.J.Skehel, R.J.Russell, and D.A.Steinhauer (2008).
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Ab initio base fragment molecular orbital studies of influenza viral hemagglutinin HA1 full-domains in complex with sialoside receptors.
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Regioselective one-pot protection of carbohydrates.
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17406895 J.Cinatl, M.Michaelis, and H.W.Doerr (2007).
The threat of avian influenza a (H5N1): part II: Clues to pathogenicity and pathology.
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The threat of avian influenza A (H5N1). Part I: Epidemiologic concerns and virulence determinants.
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17229687 J.R.Teuton, and C.R.Brandt (2007).
Sialic acid on herpes simplex virus type 1 envelope glycoproteins is required for efficient infection of cells.
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17624609 K.I.Hidari, S.Shimada, Y.Suzuki, and T.Suzuki (2007).
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Scientific barriers to developing vaccines against avian influenza viruses.
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17626098 P.Auewarakul, O.Suptawiwat, A.Kongchanagul, C.Sangma, Y.Suzuki, K.Ungchusak, S.Louisirirotchanakul, H.Lerdsamran, P.Pooruk, A.Thitithanyanont, C.Pittayawonganon, C.T.Guo, H.Hiramatsu, W.Jampangern, S.Chunsutthiwat, and P.Puthavathana (2007).
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17942670 Q.Wang, X.Tian, X.Chen, and J.Ma (2007).
Structural basis for receptor specificity of influenza B virus hemagglutinin.
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PDB codes: 2rft 2rfu
17211621 T.Korte, K.Ludwig, Q.Huang, P.S.Rachakonda, and A.Herrmann (2007).
Conformational change of influenza virus hemagglutinin is sensitive to ionic concentration.
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17540170 T.Wollert, B.Pasche, M.Rochon, S.Deppenmeier, J.van den Heuvel, A.D.Gruber, D.W.Heinz, A.Lengeling, and W.D.Schubert (2007).
Extending the host range of Listeria monocytogenes by rational protein design.
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PDB codes: 2omv 2omw 2omy
17690300 Z.Y.Yang, C.J.Wei, W.P.Kong, L.Wu, L.Xu, D.F.Smith, and G.J.Nabel (2007).
Immunization by avian H5 influenza hemagglutinin mutants with altered receptor binding specificity.
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17163385 A.Garcia-Sastre, and R.J.Whitley (2006).
Lessons learned from reconstructing the 1918 influenza pandemic.
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16415031 A.López-Bueno, M.P.Rubio, N.Bryant, R.McKenna, M.Agbandje-McKenna, and J.M.Almendral (2006).
Host-selected amino acid changes at the sialic acid binding pocket of the parvovirus capsid modulate cell binding affinity and determine virulence.
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The origin and virulence of the 1918 "Spanish" influenza virus.
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16925526 M.Knossow, and J.J.Skehel (2006).
Variation and infectivity neutralization in influenza.
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16473934 P.G.Thomas, S.A.Brown, W.Yue, J.So, R.J.Webby, and P.C.Doherty (2006).
An unexpected antibody response to an engineered influenza virus modifies CD8+ T cell responses.
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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.
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17011235 T.Horimoto, and Y.Kawaoka (2006).
Strategies for developing vaccines against H5N1 influenza A viruses.
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17027497 T.Kampmann, D.S.Mueller, A.E.Mark, P.R.Young, and B.Kobe (2006).
The Role of histidine residues in low-pH-mediated viral membrane fusion.
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16361230 T.Watabe, H.Kishino, Y.Okuhara, and Y.Kitazoe (2006).
Fold recognition of the human immunodeficiency virus type 1 V3 loop and flexibility of its crown structure during the course of adaptation to a host.
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17043214 W.P.Kong, C.Hood, Z.Y.Yang, C.J.Wei, L.Xu, A.García-Sastre, T.M.Tumpey, and G.J.Nabel (2006).
Protective immunity to lethal challenge of the 1918 pandemic influenza virus by vaccination.
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15698564 B.Chen, E.M.Vogan, H.Gong, J.J.Skehel, D.C.Wiley, and S.C.Harrison (2005).
Determining the structure of an unliganded and fully glycosylated SIV gp120 envelope glycoprotein.
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16269328 C.J.Russell, and R.G.Webster (2005).
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15731263 C.W.Lee, D.L.Suarez, T.M.Tumpey, H.W.Sung, Y.K.Kwon, Y.J.Lee, J.G.Choi, S.J.Joh, M.C.Kim, E.K.Lee, J.M.Park, X.Lu, J.M.Katz, E.Spackman, D.E.Swayne, and J.H.Kim (2005).
Characterization of highly pathogenic H5N1 avian influenza A viruses isolated from South Korea.
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16046546 D.R.Olson, L.Simonsen, P.J.Edelson, and S.S.Morse (2005).
Epidemiological evidence of an early wave of the 1918 influenza pandemic in New York City.
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15919893 E.Bianchi, X.Liang, P.Ingallinella, M.Finotto, M.A.Chastain, J.Fan, T.M.Fu, H.C.Song, M.S.Horton, D.C.Freed, W.Manger, E.Wen, L.Shi, R.Ionescu, C.Price, M.Wenger, E.A.Emini, R.Cortese, G.Ciliberto, J.W.Shiver, and A.Pessi (2005).
Universal influenza B vaccine based on the maturational cleavage site of the hemagglutinin precursor.
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15858029 K.M.Copeland, A.J.Elliot, and R.S.Daniels (2005).
Functional chimeras of human immunodeficiency virus type 1 Gp120 and influenza A virus (H3) hemagglutinin.
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Pandemic avian influenza.
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16103207 L.Glaser, J.Stevens, D.Zamarin, I.A.Wilson, A.García-Sastre, T.M.Tumpey, C.F.Basler, J.K.Taubenberger, and P.Palese (2005).
A single amino acid substitution in 1918 influenza virus hemagglutinin changes receptor binding specificity.
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15933718 L.Tang, W.R.Marion, G.Cingolani, P.E.Prevelige, and J.E.Johnson (2005).
Three-dimensional structure of the bacteriophage P22 tail machine.
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15918777 P.M.Colman (2005).
Zanamivir: an influenza virus neuraminidase inhibitor.
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Extinct 1918 virus comes alive.
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15767576 S.T.Whitten, B.García-Moreno E, and V.J.Hilser (2005).
Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins.
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16064053 T.Horimoto, and Y.Kawaoka (2005).
Influenza: lessons from past pandemics, warnings from current incidents.
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15744059 Y.Suzuki (2005).
Sialobiology of influenza: molecular mechanism of host range variation of influenza viruses.
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16014960 Z.N.Li, S.N.Mueller, L.Ye, Z.Bu, C.Yang, R.Ahmed, and D.A.Steinhauer (2005).
Chimeric influenza virus hemagglutinin proteins containing large domains of the Bacillus anthracis protective antigen: protein characterization, incorporation into infectious influenza viruses, and antigenicity.
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15556405 B.E.Collins, and J.C.Paulson (2004).
Cell surface biology mediated by low affinity multivalent protein-glycan interactions.
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15470432 D.Kobasa, A.Takada, K.Shinya, M.Hatta, P.Halfmann, S.Theriault, H.Suzuki, H.Nishimura, K.Mitamura, N.Sugaya, T.Usui, T.Murata, Y.Maeda, S.Watanabe, M.Suresh, T.Suzuki, Y.Suzuki, H.Feldmann, and Y.Kawaoka (2004).
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15563589 O.Blixt, S.Head, T.Mondala, C.Scanlan, M.E.Huflejt, R.Alvarez, M.C.Bryan, F.Fazio, D.Calarese, J.Stevens, N.Razi, D.J.Stevens, J.J.Skehel, I.van Die, D.R.Burton, I.A.Wilson, R.Cummings, N.Bovin, C.H.Wong, and J.C.Paulson (2004).
Printed covalent glycan array for ligand profiling of diverse glycan binding proteins.
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15306401 O.O'Neill (2004).
Informed consent and public health.
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Influenza: current evidence and informed predictions.
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15306391 R.M.Bush (2004).
Influenza as a model system for studying the cross-species transfer and evolution of the SARS coronavirus.
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15671756 S.Payungporn, P.Phakdeewirot, S.Chutinimitkul, A.Theamboonlers, J.Keawcharoen, K.Oraveerakul, A.Amonsin, and Y.Poovorawan (2004).
Single-step multiplex reverse transcription-polymerase chain reaction (RT-PCR) for influenza A virus subtype H5N1 detection.
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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.