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Contents |
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305 a.a.
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181 a.a.
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214 a.a.
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229 a.a.
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* Residue conservation analysis
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PDB id:
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Viral protein/immune system
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Title:
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HIV-1 hxbc2 gp120 envelope glycoprotein complexed with cd4 and induced neutralizing antibody 17b
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Structure:
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Envelope glycoprotein gp120. Chain: g. Fragment: core. Engineered: yes. Mutation: yes. T-cell surface glycoprotein cd4. Chain: c. Fragment: d1d2, n-terminal two domain fragment. Engineered: yes.
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Source:
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Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: clade b. Variant: laboratory-adapted isolate hxbc2. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Other_details: secreted from drosophila schneider 2 lines under control of an inducible metall othionein promoter. Homo sapiens.
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Biol. unit:
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Tetramer (from
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Resolution:
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2.20Å
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R-factor:
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0.268
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R-free:
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0.330
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Authors:
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P.D.Kwong,R.Wyatt,S.Majeed,J.Robinson,R.W.Sweet,J.Sodroski, W.A.Hendrickson
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Key ref:
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P.D.Kwong
et al.
(2000).
Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.
Structure,
8,
1329-1339.
PubMed id:
DOI:
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Date:
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24-Nov-00
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Release date:
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27-Dec-00
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PROCHECK
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Headers
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References
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P04578
(ENV_HV1H2) -
Envelope glycoprotein gp160 from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
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Seq:
Struc:
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856 a.a.
305 a.a.*
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P01730
(CD4_HUMAN) -
T-cell surface glycoprotein CD4 from Homo sapiens
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Seq:
Struc:
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458 a.a.
181 a.a.
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DOI no:
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Structure
8:1329-1339
(2000)
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PubMed id:
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Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.
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P.D.Kwong,
R.Wyatt,
S.Majeed,
J.Robinson,
R.W.Sweet,
J.Sodroski,
W.A.Hendrickson.
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ABSTRACT
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BACKGROUND: The gp120 exterior envelope glycoprotein of HIV-1 binds sequentially
to CD4 and chemokine receptors on cells to initiate virus entry. During natural
infection, gp120 is a primary target of the humoral immune response, and it has
evolved to resist antibody-mediated neutralization. We previously reported the
structure at 2.5 A of a gp120 core from the HXBc2 laboratory-adapted isolate in
complex with a 2 domain fragment of CD4 and the antigen binding fragment of a
human antibody. This revealed atomic details of gp120-receptor interactions and
suggested multiple mechanisms of immune evasion. RESULTS: We have now extended
the HXBc2 structure in P222, crystals to 2.2 A. The enhanced resolution enabled
a more accurate modeling of less-well-ordered regions and provided conclusive
identification of the density in the central cavity at the crux of the gp120-CD4
interaction as isopropanol from the crystallization medium. We have also
determined the structure of a gp120 core from the primary clinical HIV-1
isolate, YU2, in the same ternary complex but in a C2 crystal lattice.
Comparisons of HXBc2 and YU2 showed that while CD4 binding was rigid, portions
of the gp120 core were conformationally flexible; overall differences were
minor, with sequence changes concentrated on a surface expected to be exposed on
the envelope oligomer. CONCLUSIONS: Despite dramatic antigenic differences
between primary and laboratory-adapted HIV-1, the gp120 cores from these
isolates are remarkably similar. Taken together with chimeric substitution and
sequence analysis, this indicates that neutralization resistance is specified by
quaternary interactions involving the major variable loops and thus affords a
mechanism for viral adaptation. Conservation of the central cavity suggests the
possibility of therapeutic inhibitors. The structures reported here extend in
detail and generality our understanding of the biology of the gp120 envelope
glycoprotein.
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Selected figure(s)
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Figure 5.
Figure 5. The Central Phe-43 Cavity between CD4 and
gp120Different portions of this figure all show the Phe-43
cavity from similar orientations.(a) Ca worm diagram of the YU2
core (green) binding to CD4 (yellow). The critical Phe-43 side
chain is seen reaching into the heart of gp120. The molecular
surface of the Phe-43 cavity at the gp120-CD4 interface is
colored blue.(b) Electron density of the Phe-43 cavity. The
2F[o]-F[c] electron density is depicted at 1.1 s contour (blue).
The 2.2 Å HXBc2 structure is shown in the left panel; the 2.9 Å
YU2 structure is shown in the right panel. The HXBc2 core is
colored red; the YU2 core, green; the CD4, yellow; and the water
molecules, cyan. An isopropanol is shown at the center of the
HXBc2 cavity. It is colored yellow for carbon atoms and red for
its hydroxyl atom. CD4 residues are labeled in yellow, and YU2
residues are labeled in green.(c) Stereoplot of the HXBc2 Phe-43
cavity. The isopropanol is colored red.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
1329-1339)
copyright 2000.
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Figure was
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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A.Emileh,
and
C.F.Abrams
(2011).
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120.
|
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Proteins,
79,
537-546.
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|
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|
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|
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J.S.McLellan,
M.Pancera,
C.Carrico,
J.Gorman,
J.P.Julien,
R.Khayat,
R.Louder,
R.Pejchal,
M.Sastry,
K.Dai,
S.O'Dell,
N.Patel,
S.Shahzad-ul-Hussan,
Y.Yang,
B.Zhang,
T.Zhou,
J.Zhu,
J.C.Boyington,
G.Y.Chuang,
D.Diwanji,
I.Georgiev,
Y.D.Kwon,
D.Lee,
M.K.Louder,
S.Moquin,
S.D.Schmidt,
Z.Y.Yang,
M.Bonsignori,
J.A.Crump,
S.H.Kapiga,
N.E.Sam,
B.F.Haynes,
D.R.Burton,
W.C.Koff,
L.M.Walker,
S.Phogat,
R.Wyatt,
J.Orwenyo,
L.X.Wang,
J.Arthos,
C.A.Bewley,
J.R.Mascola,
G.J.Nabel,
W.R.Schief,
A.B.Ward,
I.A.Wilson,
and
P.D.Kwong
(2011).
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
|
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Nature,
480,
336-343.
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PDB codes:
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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.
|
| |
Proteins,
79,
1810-1819.
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|
|
|
|
|
A.Nandi,
C.L.Lavine,
P.Wang,
I.Lipchina,
P.A.Goepfert,
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D.C.Montefiori,
B.F.Haynes,
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J.G.Sodroski,
and
X.Yang
(2010).
Epitopes for broad and potent neutralizing antibody responses during chronic infection with human immunodeficiency virus type 1.
|
| |
Virology,
396,
339-348.
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C.Hager-Braun,
E.O.Hochleitner,
M.K.Gorny,
S.Zolla-Pazner,
R.J.Bienstock,
and
K.B.Tomer
(2010).
Characterization of a discontinuous epitope of the HIV envelope protein gp120 recognized by a human monoclonal antibody using chemical modification and mass spectrometric analysis.
|
| |
J Am Soc Mass Spectrom,
21,
1687-1698.
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|
|
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D.Mirano-Bascos,
N.K.Steede,
J.E.Robinson,
and
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(2010).
Influence of disulfide-stabilized structure on the specificity of helper T-cell and antibody responses to HIV envelope glycoprotein gp120.
|
| |
J Virol,
84,
3303-3311.
|
|
|
|
|
|
|
E.T.Brower,
A.Schön,
and
E.Freire
(2010).
Naturally occurring variability in the envelope glycoprotein of HIV-1 and development of cell entry inhibitors.
|
| |
Biochemistry,
49,
2359-2367.
|
|
|
|
|
|
|
H.S.Lee,
M.Contarino,
M.Umashankara,
A.Schön,
E.Freire,
A.B.Smith,
I.M.Chaiken,
and
L.S.Penn
(2010).
Use of the quartz crystal microbalance to monitor ligand-induced conformational rearrangements in HIV-1 envelope protein gp120.
|
| |
Anal Bioanal Chem,
396,
1143-1152.
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|
|
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|
|
I.Douagi,
M.N.Forsell,
C.Sundling,
S.O'Dell,
Y.Feng,
P.Dosenovic,
Y.Li,
R.Seder,
K.Loré,
J.R.Mascola,
R.T.Wyatt,
and
G.B.Karlsson Hedestam
(2010).
Influence of novel CD4 binding-defective HIV-1 envelope glycoprotein immunogens on neutralizing antibody and T-cell responses in nonhuman primates.
|
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J Virol,
84,
1683-1695.
|
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|
|
|
|
|
I.Shrivastava,
and
J.M.LaLonde
(2010).
Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network.
|
| |
Proteins,
78,
2935-2949.
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|
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|
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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,
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L.A.Lagenaur,
V.A.Villarroel,
V.Bundoc,
B.Dey,
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(2010).
sCD4-17b bifunctional protein: extremely broad and potent neutralization of HIV-1 Env pseudotyped viruses from genetically diverse primary isolates.
|
| |
Retrovirology,
7,
11.
|
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|
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|
|
M.Pancera,
S.Majeed,
Y.E.Ban,
L.Chen,
C.C.Huang,
L.Kong,
Y.D.Kwon,
J.Stuckey,
T.Zhou,
J.E.Robinson,
W.R.Schief,
J.Sodroski,
R.Wyatt,
and
P.D.Kwong
(2010).
Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.
|
| |
Proc Natl Acad Sci U S A,
107,
1166-1171.
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PDB codes:
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N.B.Siddappa,
J.D.Watkins,
K.J.Wassermann,
R.Song,
W.Wang,
V.G.Kramer,
S.Lakhashe,
M.Santosuosso,
M.C.Poznansky,
F.J.Novembre,
F.Villinger,
J.G.Else,
D.C.Montefiori,
R.A.Rasmussen,
and
R.M.Ruprecht
(2010).
R5 clade C SHIV strains with tier 1 or 2 neutralization sensitivity: tools to dissect env evolution and to develop AIDS vaccines in primate models.
|
| |
PLoS One,
5,
e11689.
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P.Wang,
and
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(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.
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| |
J Virol,
84,
7114-7123.
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|
R.Diskin,
P.M.Marcovecchio,
and
P.J.Bjorkman
(2010).
Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity.
|
| |
Nat Struct Mol Biol,
17,
608-613.
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PDB codes:
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S.Gnanakaran,
M.G.Daniels,
T.Bhattacharya,
A.S.Lapedes,
A.Sethi,
M.Li,
H.Tang,
K.Greene,
H.Gao,
B.F.Haynes,
M.S.Cohen,
G.M.Shaw,
M.S.Seaman,
A.Kumar,
F.Gao,
D.C.Montefiori,
and
B.Korber
(2010).
Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
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| |
PLoS Comput Biol,
6,
e1000955.
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S.Paul,
S.Planque,
Y.Nishiyama,
M.Escobar,
and
C.Hanson
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C.Cicala,
E.Martinelli,
J.P.McNally,
D.J.Goode,
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K.Jelicic,
S.Kottilil,
K.Macleod,
A.O'Shea,
N.Patel,
D.Van Ryk,
D.Wei,
M.Pascuccio,
L.Yi,
L.McKinnon,
P.Izulla,
J.Kimani,
R.Kaul,
A.S.Fauci,
and
J.Arthos
(2009).
The integrin {alpha}4{beta}7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1.
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| |
Proc Natl Acad Sci U S A,
106,
20877-20882.
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D.R.Davies,
B.Mamat,
O.T.Magnusson,
J.Christensen,
M.H.Haraldsson,
R.Mishra,
B.Pease,
E.Hansen,
J.Singh,
D.Zembower,
H.Kim,
A.S.Kiselyov,
A.B.Burgin,
M.E.Gurney,
and
L.J.Stewart
(2009).
Discovery of leukotriene A4 hydrolase inhibitors using metabolomics biased fragment crystallography.
|
| |
J Med Chem,
52,
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|
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PDB codes:
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E.T.Brower,
A.Schön,
J.C.Klein,
and
E.Freire
(2009).
Binding thermodynamics of the N-terminal peptide of the CCR5 coreceptor to HIV-1 envelope glycoprotein gp120.
|
| |
Biochemistry,
48,
779-785.
|
|
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|
|
|
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G.Q.Del Prete,
B.Haggarty,
G.J.Leslie,
A.P.Jordan,
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N.Wang,
J.Wang,
M.C.Holmes,
D.C.Montefiori,
and
J.A.Hoxie
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Derivation and characterization of a simian immunodeficiency virus SIVmac239 variant with tropism for CXCR4.
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J Virol,
83,
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I.Bontjer,
A.Land,
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E.Verkade,
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I.Braakman,
B.Berkhout,
and
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Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolution.
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| |
J Virol,
83,
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L.Chen,
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T.Zhou,
X.Wu,
S.O'Dell,
L.Cavacini,
A.J.Hessell,
M.Pancera,
M.Tang,
L.Xu,
Z.Y.Yang,
M.Y.Zhang,
J.Arthos,
D.R.Burton,
D.S.Dimitrov,
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R.Wyatt,
J.R.Mascola,
and
P.D.Kwong
(2009).
Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120.
|
| |
Science,
326,
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PDB codes:
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|
M.Miller
(2009).
The importance of being flexible: the case of basic region leucine zipper transcriptional regulators.
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C.H.Bell,
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Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
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PDB code:
|
|
|
|
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F.Stricher,
C.C.Huang,
A.Descours,
S.Duquesnoy,
O.Combes,
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C.Vita,
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|
| |
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382,
510-524.
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PDB codes:
|
|
|
|
|
|
|
|
H.Gopi,
M.Umashankara,
V.Pirrone,
J.LaLonde,
N.Madani,
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and
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|
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Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design.
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Science,
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PDB code:
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J.R.Mascola,
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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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| |
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