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PDBsum entry 1env
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Viral protein
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PDB id
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1env
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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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Atomic structure of the ectodomain from HIV-1 gp41
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Structure:
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HIV-1 envelope protein chimera consisting of a fragment of gcn4 zipper cloned n-terminal to two fragments of gp41. Chain: a. Fragment: gcn4 is residues 1 - 29, gp41 is residues 30 - 154. Synonym: env polyprotein. Engineered: yes. Mutation: yes
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Source:
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Fragment: 30 - 154. Saccharomyces cerevisiae, human immunodeficiency virus 1. Baker's yeast, HIV-1. Organism_taxid: 4932, 11676. Gene: gcn4, aas3, arg9, yel009c, env. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Trimer (from PDB file)
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Resolution:
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2.60Å
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R-factor:
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0.244
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R-free:
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0.277
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Authors:
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W.Weissenhorn,A.Dessen,S.C.Harrison,J.J.Skehel,D.C.Wiley
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Key ref:
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W.Weissenhorn
et al.
(1997).
Atomic structure of the ectodomain from HIV-1 gp41.
Nature,
387,
426-430.
PubMed id:
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Date:
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27-Jun-97
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Release date:
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19-Nov-97
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PROCHECK
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Headers
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References
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P03377
(ENV_HV1BR) -
Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)
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Seq:
Struc:
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861 a.a.
115 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 26 residue positions (black
crosses)
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Nature
387:426-430
(1997)
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PubMed id:
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Atomic structure of the ectodomain from HIV-1 gp41.
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W.Weissenhorn,
A.Dessen,
S.C.Harrison,
J.J.Skehel,
D.C.Wiley.
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ABSTRACT
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Fusion of viral and cellular membranes by the envelope glycoprotein gp120/gp41
effects entry of HIV-1 into the cell. The precursor, gp160, is cleaved
post-translationally into gp120 and gp41 which remain non-covalently associated.
Binding to both CD4 and a co-receptor leads to the conformational changes in
gp120/gp41 needed for membrane fusion. We used X-ray crystallography to
determine the structure of the protease-resistant part of a gp41 ectodomain
solubilized with a trimeric GCN4 coiled coil in place of the amino-terminal
fusion peptide. The core of the molecule is found to be an extended,
triple-stranded alpha-helical coiled coil with the amino terminus at its tip. A
carboxy-terminal alpha-helix packs in the reverse direction against the outside
of the coiled coil, placing the amino and carboxy termini near each other at one
end of the long rod. These features, and the existence of a similar reversal of
chain direction in the fusion pH-induced conformation of influenza virus HA2 and
in the transmembrane subunit of Moloney murine leukaemia virus (Fig. 1a-d),
suggest a common mechanism for initiating fusion.
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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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A.Engelman,
and
P.Cherepanov
(2012).
The structural biology of HIV-1: mechanistic and therapeutic insights.
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Nat Rev Microbiol,
10,
279-290.
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Y.Mao,
L.Wang,
C.Gu,
A.Herschhorn,
S.H.Xiang,
H.Haim,
X.Yang,
and
J.Sodroski
(2012).
Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
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Nat Struct Mol Biol,
19,
893-899.
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A.Ashkenazi,
and
Y.Shai
(2011).
Insights into the mechanism of HIV-1 envelope induced membrane fusion as revealed by its inhibitory peptides.
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Eur Biophys J,
40,
349-357.
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C.H.Lin,
C.H.Lin,
C.C.Chang,
T.S.Wei,
S.F.Cheng,
S.S.Chen,
and
D.K.Chang
(2011).
An efficient production and characterization of HIV-1 gp41 ectodomain with fusion peptide in Escherichia coli system.
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J Biotechnol,
153,
48-55.
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E.Khazina,
V.Truffault,
R.Büttner,
S.Schmidt,
M.Coles,
and
O.Weichenrieder
(2011).
Trimeric structure and flexibility of the L1ORF1 protein in human L1 retrotransposition.
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Nat Struct Mol Biol,
18,
1006-1014.
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PDB codes:
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I.Frank,
and
M.Robbiani
(2011).
Attachment and fusion inhibitors potently prevent dendritic cell-driven HIV infection.
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J Acquir Immune Defic Syndr,
56,
204-212.
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K.Sackett,
A.TerBush,
and
D.P.Weliky
(2011).
HIV gp41 six-helix bundle constructs induce rapid vesicle fusion at pH 3.5 and little fusion at pH 7.0: understanding pH dependence of protein aggregation, membrane binding, and electrostatics, and implications for HIV-host cell fusion.
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Eur Biophys J,
40,
489-502.
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L.T.Da,
J.M.Quan,
and
Y.D.Wu
(2011).
Understanding the binding mode and function of BMS-488043 against HIV-1 viral entry.
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Proteins,
79,
1810-1819.
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M.Caffrey
(2011).
HIV envelope: challenges and opportunities for development of entry inhibitors.
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Trends Microbiol,
19,
191-197.
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M.I.Qadir,
and
S.A.Malik
(2011).
Genetic variation in the HR region of the env gene of HIV: A perspective for resistance to HIV fusion inhibitors.
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AIDS Res Hum Retroviruses,
27,
57-63.
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M.Y.Leung,
and
F.S.Cohen
(2011).
Increasing hydrophobicity of residues in an anti-HIV-1 Env peptide synergistically improves potency.
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Biophys J,
100,
1960-1968.
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O.Chertov,
N.Zhang,
X.Chen,
J.J.Oppenheim,
J.Lubkowski,
C.McGrath,
R.C.Sowder,
B.J.Crise,
A.Malyguine,
M.A.Kutzler,
A.D.Steele,
E.E.Henderson,
and
T.J.Rogers
(2011).
Novel peptides based on HIV-1 gp120 sequence with homology to chemokines inhibit HIV infection in cell culture.
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PLoS One,
6,
e14474.
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T.Dange,
A.Joseph,
and
D.Grünwald
(2011).
A perspective of the dynamic structure of the nucleus explored at the single-molecule level.
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Chromosome Res,
19,
117-129.
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A.Finzi,
S.H.Xiang,
B.Pacheco,
L.Wang,
J.Haight,
A.Kassa,
B.Danek,
M.Pancera,
P.D.Kwong,
and
J.Sodroski
(2010).
Topological layers in the HIV-1 gp120 inner domain regulate gp41 interaction and CD4-triggered conformational transitions.
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Mol Cell,
37,
656-667.
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A.Hinz,
D.Lutje Hulsik,
A.Forsman,
W.W.Koh,
H.Belrhali,
A.Gorlani,
H.de Haard,
R.A.Weiss,
T.Verrips,
and
W.Weissenhorn
(2010).
Crystal Structure of the Neutralizing Llama V(HH) D7 and Its Mode of HIV-1 gp120 Interaction.
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PLoS One,
5,
e10482.
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PDB code:
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B.E.McGillick,
T.E.Balius,
S.Mukherjee,
and
R.C.Rizzo
(2010).
Origins of resistance to the HIVgp41 viral entry inhibitor T20.
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Biochemistry,
49,
3575-3592.
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C.R.Braun,
J.Mintseris,
E.Gavathiotis,
G.H.Bird,
S.P.Gygi,
and
L.D.Walensky
(2010).
Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome.
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Chem Biol,
17,
1325-1333.
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C.Sabin,
D.Corti,
V.Buzon,
M.S.Seaman,
D.Lutje Hulsik,
A.Hinz,
F.Vanzetta,
G.Agatic,
C.Silacci,
L.Mainetti,
G.Scarlatti,
F.Sallusto,
R.Weiss,
A.Lanzavecchia,
and
W.Weissenhorn
(2010).
Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.
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PLoS Pathog,
6,
e1001195.
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PDB code:
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D.Archary,
M.L.Gordon,
T.N.Green,
H.M.Coovadia,
P.J.Goulder,
and
T.Ndung'u
(2010).
HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression.
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Retrovirology,
7,
92.
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D.Corti,
J.P.Langedijk,
A.Hinz,
M.S.Seaman,
F.Vanzetta,
B.M.Fernandez-Rodriguez,
C.Silacci,
D.Pinna,
D.Jarrossay,
S.Balla-Jhagjhoorsingh,
B.Willems,
M.J.Zekveld,
H.Dreja,
E.O'Sullivan,
C.Pade,
C.Orkin,
S.A.Jeffs,
D.C.Montefiori,
D.Davis,
W.Weissenhorn,
A.McKnight,
J.L.Heeney,
F.Sallusto,
Q.J.Sattentau,
R.A.Weiss,
and
A.Lanzavecchia
(2010).
Analysis of memory B cell responses and isolation of novel monoclonal antibodies with neutralizing breadth from HIV-1-infected individuals.
|
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PLoS One,
5,
e8805.
|
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E.Bianchi,
J.G.Joyce,
M.D.Miller,
A.C.Finnefrock,
X.Liang,
M.Finotto,
P.Ingallinella,
P.McKenna,
M.Citron,
E.Ottinger,
R.W.Hepler,
R.Hrin,
D.Nahas,
C.Wu,
D.Montefiori,
J.W.Shiver,
A.Pessi,
and
P.S.Kim
(2010).
Vaccination with peptide mimetics of the gp41 prehairpin fusion intermediate yields neutralizing antisera against HIV-1 isolates.
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Proc Natl Acad Sci U S A,
107,
10655-10660.
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E.Gustchina,
M.Li,
J.M.Louis,
D.E.Anderson,
J.Lloyd,
C.Frisch,
C.A.Bewley,
A.Gustchina,
A.Wlodawer,
and
G.M.Clore
(2010).
Structural basis of HIV-1 neutralization by affinity matured Fabs directed against the internal trimeric coiled-coil of gp41.
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PLoS Pathog,
6,
e1001182.
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PDB codes:
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G.Frey,
J.Chen,
S.Rits-Volloch,
M.M.Freeman,
S.Zolla-Pazner,
and
B.Chen
(2010).
Distinct conformational states of HIV-1 gp41 are recognized by neutralizing and non-neutralizing antibodies.
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Nat Struct Mol Biol,
17,
1486-1491.
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PDB code:
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G.H.Bird,
N.Madani,
A.F.Perry,
A.M.Princiotto,
J.G.Supko,
X.He,
E.Gavathiotis,
J.G.Sodroski,
and
L.D.Walensky
(2010).
Hydrocarbon double-stapling remedies the proteolytic instability of a lengthy peptide therapeutic.
|
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Proc Natl Acad Sci U S A,
107,
14093-14098.
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G.Ofek,
F.J.Guenaga,
W.R.Schief,
J.Skinner,
D.Baker,
R.Wyatt,
and
P.D.Kwong
(2010).
Elicitation of structure-specific antibodies by epitope scaffolds.
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Proc Natl Acad Sci U S A,
107,
17880-17887.
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PDB codes:
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G.S.Andavan,
and
R.Lemmens-Gruber
(2010).
Cyclodepsipeptides from marine sponges: natural agents for drug research.
|
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Mar Drugs,
8,
810-834.
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H.Fausther-Bovendo,
V.Vieillard,
S.Sagan,
G.Bismuth,
and
P.Debré
(2010).
HIV gp41 engages gC1qR on CD4+ T cells to induce the expression of an NK ligand through the PIP3/H2O2 pathway.
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PLoS Pathog,
6,
e1000975.
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J.A.Thorley,
J.A.McKeating,
and
J.Z.Rappoport
(2010).
Mechanisms of viral entry: sneaking in the front door.
|
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Protoplasma,
244,
15-24.
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J.Liu,
Y.Deng,
Q.Li,
A.K.Dey,
J.P.Moore,
and
M.Lu
(2010).
Role of a putative gp41 dimerization domain in human immunodeficiency virus type 1 membrane fusion.
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J Virol,
84,
201-209.
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PDB codes:
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J.Pietzsch,
J.F.Scheid,
H.Mouquet,
M.S.Seaman,
C.C.Broder,
and
M.C.Nussenzweig
(2010).
Anti-gp41 antibodies cloned from HIV-infected patients with broadly neutralizing serologic activity.
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J Virol,
84,
5032-5042.
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J.S.Klein,
and
P.J.Bjorkman
(2010).
Few and Far Between: How HIV May Be Evading Antibody Avidity.
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PLoS Pathog,
6,
e1000908.
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K.Sackett,
M.J.Nethercott,
R.F.Epand,
R.M.Epand,
D.R.Kindra,
Y.Shai,
and
D.P.Weliky
(2010).
Comparative analysis of membrane-associated fusion peptide secondary structure and lipid mixing function of HIV gp41 constructs that model the early pre-hairpin intermediate and final hairpin conformations.
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J Mol Biol,
397,
301-315.
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L.Cai,
and
S.Jiang
(2010).
Development of peptide and small-molecule HIV-1 fusion inhibitors that target gp41.
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ChemMedChem,
5,
1813-1824.
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M.Hertje,
M.Zhou,
and
U.Dietrich
(2010).
Inhibition of HIV-1 entry: multiple keys to close the door.
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ChemMedChem,
5,
1825-1835.
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M.I.Qadir,
and
S.A.Malik
(2010).
HIV fusion inhibitors.
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Rev Med Virol,
20,
23-33.
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M.L.Bellows,
and
C.A.Floudas
(2010).
Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.
|
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Curr Drug Targets,
11,
264-278.
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M.M.Freeman,
M.S.Seaman,
S.Rits-Volloch,
X.Hong,
C.Y.Kao,
D.D.Ho,
and
B.Chen
(2010).
Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody.
|
| |
Structure,
18,
1632-1641.
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PDB code:
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M.Umashankara,
K.McFadden,
I.Zentner,
A.Schön,
S.Rajagopal,
F.Tuzer,
S.A.Kuriakose,
M.Contarino,
J.Lalonde,
E.Freire,
and
I.Chaiken
(2010).
The active core in a triazole peptide dual-site antagonist of HIV-1 gp120.
|
| |
ChemMedChem,
5,
1871-1879.
|
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N.González,
M.Pérez-Olmeda,
E.Mateos,
A.Cascajero,
A.Alvarez,
S.Spijkers,
J.García-Pérez,
S.Sánchez-Palomino,
E.Ruiz-Mateos,
M.Leal,
and
J.Alcami
(2010).
A sensitive phenotypic assay for the determination of human immunodeficiency virus type 1 tropism.
|
| |
J Antimicrob Chemother,
65,
2493-2501.
|
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|
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P.Wang,
and
X.Yang
(2010).
Neutralization efficiency is greatly enhanced by bivalent binding of an antibody to epitopes in the V4 region and the membrane-proximal external region within one trimer of human immunodeficiency virus type 1 glycoproteins.
|
| |
J Virol,
84,
7114-7123.
|
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R.Song,
D.Franco,
C.Y.Kao,
F.Yu,
Y.Huang,
and
D.D.Ho
(2010).
Epitope mapping of ibalizumab, a humanized Anti-CD4 monoclonal antibody with anti-HIV-1 activity in infected patients.
|
| |
J Virol,
84,
6935-6942.
|
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S.R.Wu,
R.Löving,
B.Lindqvist,
H.Hebert,
P.J.Koeck,
M.Sjöberg,
and
H.Garoff
(2010).
Single-particle cryoelectron microscopy analysis reveals the HIV-1 spike as a tripod structure.
|
| |
Proc Natl Acad Sci U S A,
107,
18844-18849.
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V.Buzon,
G.Natrajan,
D.Schibli,
F.Campelo,
M.M.Kozlov,
and
W.Weissenhorn
(2010).
Crystal structure of HIV-1 gp41 including both fusion peptide and membrane proximal external regions.
|
| |
PLoS Pathog,
6,
e1000880.
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PDB code:
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X.Shen,
S.M.Dennison,
P.Liu,
F.Gao,
F.Jaeger,
D.C.Montefiori,
L.Verkoczy,
B.F.Haynes,
S.M.Alam,
and
G.D.Tomaras
(2010).
Prolonged exposure of the HIV-1 gp41 membrane proximal region with L669S substitution.
|
| |
Proc Natl Acad Sci U S A,
107,
5972-5977.
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X.Zhang,
M.Boyce,
B.Bhattacharya,
X.Zhang,
S.Schein,
P.Roy,
and
Z.H.Zhou
(2010).
Bluetongue virus coat protein VP2 contains sialic acid-binding domains, and VP5 resembles enveloped virus fusion proteins.
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| |
Proc Natl Acad Sci U S A,
107,
6292-6297.
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PDB code:
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Y.Wang,
H.Lu,
Q.Zhu,
S.Jiang,
and
Y.Liao
(2010).
Structure-based design, synthesis and biological evaluation of new N-carboxyphenylpyrrole derivatives as HIV fusion inhibitors targeting gp41.
|
| |
Bioorg Med Chem Lett,
20,
189-192.
|
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Y.Zhu,
L.Lu,
L.Xu,
H.Yang,
S.Jiang,
and
Y.H.Chen
(2010).
Identification of a gp41 core-binding molecule with homologous sequence of human TNNI3K-like protein as a novel human immunodeficiency virus type 1 entry inhibitor.
|
| |
J Virol,
84,
9359-9368.
|
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A.C.Oliveira,
A.N.Martins,
A.F.Pires,
M.B.Arruda,
A.Tanuri,
H.S.Pereira,
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J.A.Hoxie,
and
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(1997).
Promiscuous use of CC and CXC chemokine receptors in cell-to-cell fusion mediated by a human immunodeficiency virus type 2 envelope protein.
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J Virol,
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R.C.Lin,
and
R.H.Scheller
(1997).
Structural organization of the synaptic exocytosis core complex.
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Neuron,
19,
1087-1094.
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S.R.Durell,
I.Martin,
J.M.Ruysschaert,
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and
R.Blumenthal
(1997).
What studies of fusion peptides tell us about viral envelope glycoprotein-mediated membrane fusion (review).
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Mol Membr Biol,
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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
