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Contents |
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(+ 3 more)
322 a.a.
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(+ 3 more)
175 a.a.
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* Residue conservation analysis
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PDB id:
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Viral protein
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Title:
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Crystal structure of a h5n1 influenza virus hemagglutinin.
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Structure:
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Hemagglutinin. Chain: a, c, e, g, i, k, m, o, q. Fragment: receptor binding domain, ha14. Engineered: yes. Hemagglutinin. Chain: b, d, f, h, j, l, n, p, r. Fragment: membrane fusion domain, ha2. Engineered: yes
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Source:
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Influenza a virus (a/viet nam/1203/2004(h5n1)). Organism_taxid: 284218. Strain: a/vietnam/1203/2004. Expressed in: trichoplusia ni. Expression_system_taxid: 7111.
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Biol. unit:
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Hexamer (from PDB file)
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Resolution:
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2.95Å
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R-factor:
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0.269
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R-free:
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0.319
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Authors:
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J.Stevens,I.A.Wilson
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Key ref:
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J.Stevens
et al.
(2006).
Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus.
Science,
312,
404-410.
PubMed id:
DOI:
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Date:
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03-Jan-06
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Release date:
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02-May-06
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PROCHECK
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Headers
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References
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DOI no:
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Science
312:404-410
(2006)
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PubMed id:
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Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus.
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J.Stevens,
O.Blixt,
T.M.Tumpey,
J.K.Taubenberger,
J.C.Paulson,
I.A.Wilson.
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ABSTRACT
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The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly
pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and
other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this
Viet04 HA reveals an avian alpha2-3 sialic acid receptor binding preference.
Introduction of mutations that can convert H1 serotype HAs to human alpha2-6
receptor specificity only enhanced or reduced affinity for avian-type receptors.
However, mutations that can convert avian H2 and H3 HAs to human receptor
specificity, when inserted onto the Viet04 H5 HA framework, permitted binding to
a natural human alpha2-6 glycan, which suggests a path for this H5N1 virus to
gain a foothold in the human population.
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Selected figure(s)
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Figure 1.
Fig. 1. Crystal structure of Viet04 HA and comparison with 1918
human H1, duck H5, and 1968 human H3 HAs. (A) Overview of the
Viet04 trimer, represented as a ribbon diagram. For clarity,
each monomer has been colored differently. Carbohydrates
observed in the electron-density maps are colored orange, and
all the asparagines that make up a glycosylation site are
labeled. Only Glu20, Glu289, and Phe^154 are not labeled, as
these are on the back of the molecule. The location of the
receptor binding, cleavage, and basic patch sites are
highlighted only on one monomer. All the figures were generated
and rendered with the use of MacPymol (66). (B) Structural
comparison of the Viet04 monomer (olive) with duck H5 (orange)
and 1918 H1 (red) HAs. Structures were first superimposed on the
HA2 domain of Viet04 through the following residues: Viet04,
Gly1 to Pro160; 1918 H1 (PDB: 1rd8), Gly1 to Pro160;
H3(PDB:2hmg), Gly1 to Pro160; H5 (PDB: 1jsm [PDB]
), Gly1 to Pro160. Orientation of the overlay approximates to
the blue monomer in (A). (C) Superimposition of the two long
 -helices of HA2
for 1918 H1 (PDB: 1rd8), avian H5 (PDB: 1jsm [PDB]
), human H3 (PDB: 2hmg [PDB]
), and Viet04 reveal that the extended interhelical loop of
Viet04 is more similar to the 1918 H1 than to the existing avian
H5 structure. The side chain of Phe^63 is illustrated as an
example of the close proximity of the two structures.
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Figure 2.
Fig. 2. Antigenic variation in recent H5N1 viruses mapped onto
the Viet04 structure. (Left) Side view of the Viet04 structure
in which natural mutations identified by comparison of 2005 with
2004 isolates (23) are colored yellow; escape mutants (24, 25)
are blue; and those that overlap in both analyses are green. All
of the 2004 and 2005 strains have a new potential glycosylation
site at position 158 in the HA1 chain (orange). The receptor
binding site is highlighted with a red oval. (Right) Top view
looking down onto the globular membrane distal end of the trimer
around the RBD showing that the mutations mainly cluster around
the RBD.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2006,
312,
404-410)
copyright 2006.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.M.Morens,
K.Subbarao,
and
J.K.Taubenberger
(2012).
Engineering H5N1 avian influenza viruses to study human adaptation.
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Nature,
486,
335-340.
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|
|
|
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M.Imai,
T.Watanabe,
M.Hatta,
S.C.Das,
M.Ozawa,
K.Shinya,
G.Zhong,
A.Hanson,
H.Katsura,
S.Watanabe,
C.Li,
E.Kawakami,
S.Yamada,
M.Kiso,
Y.Suzuki,
E.A.Maher,
G.Neumann,
and
Y.Kawaoka
(2012).
Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets.
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Nature,
486,
420-428.
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|
|
|
|
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D.M.Tscherne,
and
A.García-Sastre
(2011).
Virulence determinants of pandemic influenza viruses.
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J Clin Invest,
121,
6.
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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.
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J Antimicrob Chemother,
66,
15-28.
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H.Shelton,
G.Ayora-Talavera,
J.Ren,
S.Loureiro,
R.J.Pickles,
W.S.Barclay,
and
I.M.Jones
(2011).
Receptor binding profiles of avian influenza virus hemagglutinin subtypes on human cells as a predictor of pandemic potential.
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J Virol,
85,
1875-1880.
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J.Abdussamad,
and
S.Aris-Brosou
(2011).
The nonadaptive nature of the H1N1 2009 Swine Flu pandemic contrasts with the adaptive facilitation of transmission to a new host.
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BMC Evol Biol,
11,
6.
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J.L.Wasilenko,
A.M.Arafa,
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A.Balish,
A.Klimov,
D.L.Suarez,
D.E.Swayne,
and
M.J.Pantin-Jackwood
(2011).
Pathogenicity of two Egyptian H5N1 highly pathogenic avian influenza viruses in domestic ducks.
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Arch Virol,
156,
37-51.
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J.Wei,
B.Yan,
Z.Chen,
T.Li,
F.Deng,
H.Wang,
and
Z.Hu
(2011).
Production and characterization of monoclonal antibodies against the hemagglutinin of H5N1 and antigenic investigation of avian influenza H5N1 viruses isolated from China.
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Can J Microbiol,
57,
42-48.
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K.T.Huang,
K.Gorska,
S.Alvarez,
S.Barluenga,
and
N.Winssinger
(2011).
Combinatorial self-assembly of glycan fragments into microarrays.
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Chembiochem,
12,
56-60.
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M.W.Chen,
H.Y.Liao,
Y.Huang,
J.T.Jan,
C.C.Huang,
C.T.Ren,
C.Y.Wu,
T.J.Cheng,
D.D.Ho,
and
C.H.Wong
(2011).
Broadly neutralizing DNA vaccine with specific mutation alters the antigenicity and sugar-binding activities of influenza hemagglutinin.
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Proc Natl Acad Sci U S A,
108,
3510-3515.
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N.Goñi,
G.Moratorio,
V.Ramas,
L.Coppola,
H.Chiparelli,
and
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(2011).
Phylogenetic analysis of pandemic 2009 influenza A virus circulating in the South American region: genetic relationships and vaccine strain match.
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Arch Virol,
156,
87-94.
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R.A.Medina,
and
A.García-Sastre
(2011).
Influenza A viruses: new research developments.
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Nat Rev Microbiol,
9,
590-603.
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|
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S.Ge,
and
Z.Wang
(2011).
An overview of influenza A virus receptors.
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Crit Rev Microbiol,
37,
157-165.
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S.J.Drews,
K.Pabbaraju,
S.Wong,
K.L.Tokaryk,
J.May-Hadford,
B.Lee,
R.Tellier,
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Surveillance of autopsy cases for D222G substitutions in haemagglutinin of the pandemic (H1N1) 2009 virus in Alberta, Canada.
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Clin Microbiol Infect,
17,
582-584.
|
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|
|
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T.R.Maines,
L.M.Chen,
N.Van Hoeven,
T.M.Tumpey,
O.Blixt,
J.A.Belser,
K.M.Gustin,
M.B.Pearce,
C.Pappas,
J.Stevens,
N.J.Cox,
J.C.Paulson,
R.Raman,
R.Sasisekharan,
J.M.Katz,
and
R.O.Donis
(2011).
Effect of receptor binding domain mutations on receptor binding and transmissibility of avian influenza H5N1 viruses.
|
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Virology,
413,
139-147.
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A.L.Balish,
C.T.Davis,
M.D.Saad,
N.El-Sayed,
H.Esmat,
J.A.Tjaden,
K.C.Earhart,
L.E.Ahmed,
M.Abd El-Halem,
A.H.Ali,
S.A.Nassif,
E.A.El-Ebiary,
M.Taha,
M.M.Aly,
A.Arafa,
E.O'Neill,
X.Xiyan,
N.J.Cox,
R.O.Donis,
and
A.I.Klimov
(2010).
Antigenic and genetic diversity of highly pathogenic avian influenza A (H5N1) viruses isolated in Egypt.
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Avian Dis,
54,
329-334.
|
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|
|
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|
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A.S.Abdel-Moneim,
A.E.Abdel-Ghany,
and
S.A.Shany
(2010).
Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys.
|
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J Biomed Sci,
17,
25.
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B.Mänz,
M.Matrosovich,
N.Bovin,
and
M.Schwemmle
(2010).
A polymorphism in the hemagglutinin of the human isolate of a highly pathogenic H5N1 influenza virus determines organ tropism in mice.
|
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J Virol,
84,
8316-8321.
|
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|
|
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|
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F.He,
R.D.Soejoedono,
S.Murtini,
M.Goutama,
and
J.Kwang
(2010).
Complementary monoclonal antibody-based dot ELISA for universal detection of H5 avian influenza virus.
|
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BMC Microbiol,
10,
330.
|
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|
|
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|
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H.Achdout,
T.Meningher,
S.Hirsh,
A.Glasner,
Y.Bar-On,
C.Gur,
A.Porgador,
M.Mendelson,
M.Mandelboim,
and
O.Mandelboim
(2010).
Killing of avian and Swine influenza virus by natural killer cells.
|
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J Virol,
84,
3993-4001.
|
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|
|
|
|
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H.L.Oh,
S.Akerström,
S.Shen,
S.Bereczky,
H.Karlberg,
J.Klingström,
S.K.Lal,
A.Mirazimi,
and
Y.J.Tan
(2010).
An antibody against a novel and conserved epitope in the hemagglutinin 1 subunit neutralizes numerous H5N1 influenza viruses.
|
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J Virol,
84,
8275-8286.
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|
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|
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H.M.Weingartl
(2010).
Did the 2009 pandemic influenza virus originate in humans?
|
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Future Microbiol,
5,
989-991.
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|
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H.M.Yassine,
C.W.Lee,
R.Gourapura,
and
Y.M.Saif
(2010).
Interspecies and intraspecies transmission of influenza A viruses: viral, host and environmental factors.
|
| |
Anim Health Res Rev,
11,
53-72.
|
|
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|
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H.M.Yassine,
M.Khatri,
C.W.Lee,
and
Y.M.Saif
(2010).
Characterization of an H3N2 triple reassortant influenza virus with a mutation at the receptor binding domain (D190A) that occurred upon virus transmission from turkeys to pigs.
|
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Virol J,
7,
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|
|
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|
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H.Yang,
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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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PLoS Pathog,
6,
e1001081.
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PDB codes:
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|
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H.Yang,
P.Carney,
and
J.Stevens
(2010).
Structure and Receptor binding properties of a pandemic H1N1 virus hemagglutinin.
|
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PLoS Curr,
2,
RRN1152.
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PDB code:
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I.A.Rudneva,
A.A.Kushch,
O.V.Masalova,
T.A.Timofeeva,
R.R.Klimova,
A.A.Shilov,
A.V.Ignatieva,
P.S.Krylov,
and
N.V.Kaverin
(2010).
Antigenic epitopes in the hemagglutinin of Qinghai-type influenza H5N1 virus.
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Viral Immunol,
23,
181-187.
|
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|
|
|
|
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J.Stevens,
L.M.Chen,
P.J.Carney,
R.Garten,
A.Foust,
J.Le,
B.A.Pokorny,
R.Manojkumar,
J.Silverman,
R.Devis,
K.Rhea,
X.Xu,
D.J.Bucher,
J.C.Paulson,
J.Paulson,
N.J.Cox,
A.Klimov,
and
R.O.Donis
(2010).
Receptor specificity of influenza A H3N2 viruses isolated in mammalian cells and embryonated chicken eggs.
|
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J Virol,
84,
8287-8299.
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K.J.Vandegrift,
S.H.Sokolow,
P.Daszak,
and
A.M.Kilpatrick
(2010).
Ecology of avian influenza viruses in a changing world.
|
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Ann N Y Acad Sci,
1195,
113-128.
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A.Chandrasekaran,
A.Srinivasan,
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V.Sasisekharan,
and
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(2010).
Glycans as receptors for influenza pathogenesis.
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Glycoconj J,
27,
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E.A.Govorkova,
R.G.Webster,
and
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(2010).
The pH of activation of the hemagglutinin protein regulates H5N1 influenza virus pathogenicity and transmissibility in ducks.
|
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J Virol,
84,
1527-1535.
|
|
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|
|
|
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N.Parera Pera,
H.M.Branderhorst,
R.Kooij,
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R.Ruijtenbeek,
and
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(2010).
Rapid screening of lectins for multivalency effects with a glycodendrimer microarray.
|
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Chembiochem,
11,
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|
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and
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(2010).
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|
| |
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|
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and
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Structure, receptor binding, and antigenicity of influenza virus hemagglutinins from the 1957 H2N2 pandemic.
|
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PDB codes:
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|
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S.Chutinimitkul,
D.van Riel,
V.J.Munster,
J.M.van den Brand,
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and
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| |
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and
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(2010).
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|
| |
J Biol Chem,
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| |
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| |
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|
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W.M.Jiang,
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|
| |
J Gen Virol,
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|
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|
|
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and
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(2010).
Glycosylation at 158N of the hemagglutinin protein and receptor binding specificity synergistically affect the antigenicity and immunogenicity of a live attenuated H5N1 A/Vietnam/1203/2004 vaccine virus in ferrets.
|
| |
J Virol,
84,
6570-6577.
|
|
|
|
|
|
|
Y.Berhane,
M.Leith,
C.Embury-Hyatt,
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T.Hisanaga,
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K.Hooper-McGrevy,
and
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(2010).
Studying possible cross-protection of Canada geese preexposed to North American low pathogenicity avian influenza virus strains (H3N8, H4N6, and H5N2) against an H5N1 highly pathogenic avian influenza challenge.
|
| |
Avian Dis,
54,
548-554.
|
|
|
|
|
|
|
Y.Monteerarat,
O.Suptawiwat,
C.Boonarkart,
M.Uiprasertkul,
P.Auewarakul,
and
V.Viprakasit
(2010).
Inhibition of H5N1 highly pathogenic influenza virus by suppressing a specific sialyltransferase.
|
| |
Arch Virol,
155,
889-893.
|
|
|
|
|
|
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Y.Piwpankaew,
Y.Monteerarat,
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PDB codes:
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R.G.Wallace,
H.Hodac,
R.H.Lathrop,
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S.Hanashima,
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S.Perk,
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Virus Genes,
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T.J.Dickerson,
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Phage escape libraries for checkmate analysis.
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Proc Natl Acad Sci U S A,
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(2007).
Extending the host range of Listeria monocytogenes by rational protein design.
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Cell,
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PDB codes:
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U.B.Aamir,
U.Wernery,
N.Ilyushina,
and
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Photogenerated carbohydrate microarrays.
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M.Kiso,
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Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors.
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Nature,
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PDB code:
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T.R.Maines,
L.M.Chen,
Y.Matsuoka,
H.Chen,
T.Rowe,
J.Ortin,
A.Falcón,
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Lack of transmission of H5N1 avian-human reassortant influenza viruses in a ferret model.
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Proc Natl Acad Sci U S A,
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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.
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Links
