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* Residue conservation analysis
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PDB id:
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Immune system
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Title:
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Crystal structure analysis of anti-HIV-1 fab 447-52d in complex with v3 peptide
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Structure:
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Fab 447-52d, light chain. Chain: l, m. Fab 447-52d, heavy chain. Chain: h, i. Gp120 v3 peptide. Chain: p, q. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Organ: blood. Other_details: isolated from peripheral blood cells. Synthetic: yes. Other_details: this sequence occurs in HIV-1 gp120
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Biol. unit:
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Trimer (from
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Resolution:
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2.50Å
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R-factor:
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0.250
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R-free:
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0.285
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Authors:
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R.L.Stanfield,M.K.Gorny,C.Williams,S.Zolla-Pazner,I.A.Wilson
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Key ref:
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R.L.Stanfield
et al.
(2004).
Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.
Structure,
12,
193-204.
PubMed id:
DOI:
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Date:
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21-Jul-03
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Release date:
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17-Feb-04
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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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Structure
12:193-204
(2004)
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PubMed id:
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Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.
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R.L.Stanfield,
M.K.Gorny,
C.Williams,
S.Zolla-Pazner,
I.A.Wilson.
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ABSTRACT
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447-52D is a human monoclonal antibody isolated from a heterohybridoma derived
from an HIV-1-infected individual. This antibody recognizes the hypervariable
gp120 V3 loop, and neutralizes both X4 and R5 primary isolates, making it one of
the most effective anti-V3 antibodies characterized to date. The crystal
structure of the 447-52D Fab in complex with a 16-mer V3 peptide at 2.5 A
resolution reveals that the peptide beta hairpin forms a three-stranded mixed
beta sheet with complementarity determining region (CDR) H3, with most of the V3
side chains exposed to solvent. Sequence specificity is conferred through
interaction of the type-II turn (residues GPGR) at the apex of the V3 hairpin
with the base of CDR H3. This novel mode of peptide-antibody recognition enables
the antibody to bind to many different V3 sequences where only the GPxR core
epitope is absolutely required.
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Selected figure(s)
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Figure 6.
Figure 6. Stereo view of the Fab 447-52D Antigen Binding
Site(A) As in all figures except Figure 1, the Fab light and
heavy chains are depicted in salmon and blue, with the bound
peptide in yellow. The side chains of the Fab residues in
contact with peptide are shown in a ball-and-stick
representation.(B) A magnified view of the cation-p and salt
bridge interactions between peptide and Fab. The V3 peptide
residue ArgP315 forms a salt bridge with AspH95, and makes
cation-p interactions with the side chains of TyrH100j and
TrpH33. Peptide residue ProP313 is nestled into a cleft formed
by Fab residues TrpL91 and TrpL96, with the Pro ring nearly
coplanar to the TrpL91 indole.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2004,
12,
193-204)
copyright 2004.
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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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J.S.McLellan,
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I.A.Wilson,
and
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(2011).
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
|
| |
Nature,
480,
336-343.
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|
|
PDB codes:
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A.Nandi,
C.L.Lavine,
P.Wang,
I.Lipchina,
P.A.Goepfert,
G.M.Shaw,
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and
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| |
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and
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(2010).
Anti-V3 monoclonal antibodies display broad neutralizing activities against multiple HIV-1 subtypes.
|
| |
PLoS One,
5,
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D.Almond,
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and
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(2010).
Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop.
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| |
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and
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Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
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PLoS Comput Biol,
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Back to the future: covalent epitope-based HIV vaccine development.
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Expert Rev Vaccines,
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S.Zolla-Pazner,
and
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Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design.
|
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Nat Rev Immunol,
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and
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(2010).
Conserved structural elements in the V3 crown of HIV-1 gp120.
|
| |
Nat Struct Mol Biol,
17,
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|
|
|
PDB codes:
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|
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|
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A.Mor,
E.Segal,
B.Mester,
B.Arshava,
O.Rosen,
F.X.Ding,
J.Russo,
A.Dafni,
F.Schvartzman,
T.Scherf,
F.Naider,
and
J.Anglister
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Mimicking the structure of the V3 epitope bound to HIV-1 neutralizing antibodies.
|
| |
Biochemistry,
48,
3288-3303.
|
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|
|
E.S.Gray,
N.Taylor,
D.Wycuff,
P.L.Moore,
G.D.Tomaras,
C.K.Wibmer,
A.Puren,
A.DeCamp,
P.B.Gilbert,
B.Wood,
D.C.Montefiori,
J.M.Binley,
G.M.Shaw,
B.F.Haynes,
J.R.Mascola,
and
L.Morris
(2009).
Antibody specificities associated with neutralization breadth in plasma from human immunodeficiency virus type 1 subtype C-infected blood donors.
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J Virol,
83,
8925-8937.
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J.Takehisa,
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A.Ayouba,
E.Bailes,
F.Van Heuverswyn,
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P.M.Sharp,
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Origin and biology of simian immunodeficiency virus in wild-living western gorillas.
|
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J Virol,
83,
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K.L.Davis,
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H.Li,
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J Virol,
83,
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and
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NMR evidence of charge-dependent interaction between various PND V3 and CCR5 N-terminal peptides.
|
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Biopolymers,
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94.
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P.D.Kwong,
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HIV-1 and influenza antibodies: seeing antigens in new ways.
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| |
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M.Lu,
P.J.Klasse,
and
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Two HIV-1 variants resistant to small molecule CCR5 inhibitors differ in how they use CCR5 for entry.
|
| |
PLoS Pathog,
5,
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|
R.Pejchal,
J.S.Gach,
F.M.Brunel,
R.M.Cardoso,
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P.E.Dawson,
D.R.Burton,
M.B.Zwick,
and
I.A.Wilson
(2009).
A conformational switch in human immunodeficiency virus gp41 revealed by the structures of overlapping epitopes recognized by neutralizing antibodies.
|
| |
J Virol,
83,
8451-8462.
|
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PDB code:
|
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|
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|
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T.Cardozo,
J.Swetnam,
A.Pinter,
C.Krachmarov,
A.Nadas,
D.Almond,
and
S.Zolla-Pazner
(2009).
Worldwide distribution of HIV type 1 epitopes recognized by human anti-V3 monoclonal antibodies.
|
| |
AIDS Res Hum Retroviruses,
25,
441-450.
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|
|
|
|
|
|
V.Burke,
C.Williams,
M.Sukumaran,
S.S.Kim,
H.Li,
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M.K.Gorny,
S.Zolla-Pazner,
and
X.P.Kong
(2009).
Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens.
|
| |
Structure,
17,
1538-1546.
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PDB codes:
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Y.Nishiyama,
S.Planque,
Y.Mitsuda,
G.Nitti,
H.Taguchi,
L.Jin,
J.Symersky,
S.Boivin,
M.Sienczyk,
M.Salas,
C.V.Hanson,
and
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(2009).
Toward effective HIV vaccination: induction of binary epitope reactive antibodies with broad HIV neutralizing activity.
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| |
J Biol Chem,
284,
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R.L.Stanfield,
M.K.Gorny,
C.Williams,
S.Zolla-Pazner,
and
I.A.Wilson
(2008).
Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.
|
| |
Acta Crystallogr D Biol Crystallogr,
64,
792-802.
|
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PDB code:
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|
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C.H.Bell,
R.Pantophlet,
A.Schiefner,
L.A.Cavacini,
R.L.Stanfield,
D.R.Burton,
and
I.A.Wilson
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Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
|
| |
J Mol Biol,
375,
969-978.
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PDB code:
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D.Kuroda,
H.Shirai,
M.Kobori,
and
H.Nakamura
(2008).
Structural classification of CDR-H3 revisited: a lesson in antibody modeling.
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| |
Proteins,
73,
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A.Kuehne,
D.M.Abelson,
M.L.Fusco,
M.K.Hart,
and
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(2008).
Complex of a protective antibody with its Ebola virus GP peptide epitope: unusual features of a V lambda x light chain.
|
| |
J Mol Biol,
375,
202-216.
|
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PDB code:
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M.B.Patel,
N.G.Hoffman,
and
R.Swanstrom
(2008).
Subtype-specific conformational differences within the V3 region of subtype B and subtype C human immunodeficiency virus type 1 Env proteins.
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| |
J Virol,
82,
903-916.
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|
|
M.L.Visciano,
M.Tuen,
P.D.Chen,
and
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Antibodies to the CD4-binding site of HIV-1 gp120 suppress gp120-specific CD4 T cell response while enhancing antibody response.
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| |
Infect Agent Cancer,
3,
11.
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M.Montero,
N.E.van Houten,
X.Wang,
and
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The membrane-proximal external region of the human immunodeficiency virus type 1 envelope: dominant site of antibody neutralization and target for vaccine design.
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Microbiol Mol Biol Rev,
72,
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M.Vaine,
S.Wang,
E.T.Crooks,
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Improved induction of antibodies against key neutralizing epitopes by human immunodeficiency virus type 1 gp120 DNA prime-protein boost vaccination compared to gp120 protein-only vaccination.
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J Virol,
82,
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H.Wessner,
K.Welfle,
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C.Scholz,
M.Seifert,
K.Zubow,
J.Aÿ,
M.Hahn,
P.Scheerer,
A.Skerra,
and
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(2008).
The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops.
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| |
Proteins,
73,
552-565.
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PDB codes:
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P.Nyambi,
S.Burda,
M.Urbanski,
L.Heyndrickx,
W.Janssens,
G.Vanham,
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Neutralization patterns and evolution of sequential HIV type 1 envelope sequences in HIV type 1 subtype B-infected drug-naive individuals.
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AIDS Res Hum Retroviruses,
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T.Wrin,
L.A.Cavacini,
J.E.Robinson,
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D.R.Burton
(2008).
Neutralizing activity of antibodies to the V3 loop region of HIV-1 gp120 relative to their epitope fine specificity.
|
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Virology,
381,
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M.Landersz,
B.Rodes,
V.Soriano,
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M.T.Dittmar,
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| |
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|
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| |
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71,
906-914.
|
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M.A.Luftig,
M.Mattu,
P.Di Giovine,
R.Geleziunas,
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M.D.Miller,
A.Pessi,
and
A.Carfí
(2006).
Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody.
|
| |
Nat Struct Mol Biol,
13,
740-747.
|
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PDB code:
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|
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|
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M.K.Gorny,
C.Williams,
B.Volsky,
K.Revesz,
X.H.Wang,
S.Burda,
T.Kimura,
F.A.Konings,
A.Nádas,
C.A.Anyangwe,
P.Nyambi,
C.Krachmarov,
A.Pinter,
and
S.Zolla-Pazner
(2006).
Cross-clade neutralizing activity of human anti-V3 monoclonal antibodies derived from the cells of individuals infected with non-B clades of human immunodeficiency virus type 1.
|
| |
J Virol,
80,
6865-6872.
|
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|
|
|
|
|
R.L.Stanfield,
M.K.Gorny,
S.Zolla-Pazner,
and
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(2006).
Crystal structures of human immunodeficiency virus type 1 (HIV-1) neutralizing antibody 2219 in complex with three different V3 peptides reveal a new binding mode for HIV-1 cross-reactivity.
|
| |
J Virol,
80,
6093-6105.
|
|
|
PDB codes:
|
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|
|
|
|
|
|
R.Pantophlet,
and
D.R.Burton
(2006).
GP120: target for neutralizing HIV-1 antibodies.
|
| |
Annu Rev Immunol,
24,
739-769.
|
|
|
|
|
|
|
V.Choudhry,
M.Y.Zhang,
D.Dimitrova,
P.Prabakaran,
A.S.Dimitrov,
T.R.Fouts,
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D.S.Dimitrov
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|
| |
Expert Opin Biol Ther,
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523-531.
|
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A.de Parseval,
M.D.Bobardt,
A.Chatterji,
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M.Farzan,
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PDB code:
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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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