Primary Citation PubMed: 22451932
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CD4 binding determinant mimicry for HIV vaccine design.
(2012) Front Immunol 3
PubMed: 23251137 | PubMedCentral: PMC3523313 | DOI: 10.3389/fimmu.2012.00383
(A) Superimposed CD4BD core conformations in gp120 variants (residues 421–433) complexed with soluble CD4 and antibody 17b (cyan; 1GC1) and gp120 (extended core) without a ligand (purple; 3TGQ... 3TGR, 3TGT, 3TIH).
, CD4 liganded 1GC1, 1G9M, 1G9N, 1RZJ, 1RZK, 3JWD, 3JWO, 2NXY, 2NXZ, 2NY5, 2B4C, 2QAD; unliganded 2BF1, 3TGQ, 3TGR, 3TGT, 3TIH; CD4BD OD antibody liganded 3NGB, 3SE8, 3SE9, 3U7Y, 2NY7, 3HI1, 3IDX; low-molecular-weight CD4 mimetic liganded 1YYL, 1YYM, 2I5Y, 2I60, 3TGS).
Publication Year: 2012
Epitope specificity of human immunodeficiency virus-1 antibody dependent cellular cytotoxicity [ADCC] responses.
(2013) Curr HIV Res 11
PubMed: 24191939 | PubMedCentral: PMC3878369 | DOI: null
X-ray coordinates of (A) the unliganded gp12093TH057 coree (PDB:3TGT) and (B) the gp120HXBc2core/s CD4 subset of gp120HXBc2core/CD4/17b complex (PDB:1GC1) were fitted into tomograms using Chimera ...
Publication Year: 2013
Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.
(2014) PLoS One 9
PubMed: 24489681 | PubMedCentral: PMC3904841 | DOI: 10.1371/journal.pone.0085940
The structure of YU2core-NBD-557-48d complex was solved by molecular replacement using gp120 structure in complex with CD4 and 17b (PDB ID: 1RZK) as a search model, and structures of other small molec... le bound-clade A/E gp120 93TH057 H375S complexes were solved by molecular replacement using AutoMR in PHENIX software suite  with unliganded clade A/E gp120 core e (PDB ID: 3TGT) as a search model.
Publication Year: 2014
Tertiary structure-based prediction of conformational B-cell epitopes through B factors.
(2014) Bioinformatics 30
PubMed: 24931993 | PubMedCentral: PMC4058920 | DOI: 10.1093/bioinformatics/btu281
4.1 Antigen GP120 of HIV-1 clade A/E 93TH057 The tertiary structure data of the antigen GP120 of HIV-1 clade A/E 93TH057 is stored at PDB entry 3TGT.
NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences.
(2014) Nucleic Acids Res 42
PubMed: 24782517 | PubMedCentral: PMC4086065 | DOI: 10.1093/nar/gku318
Based on VRC01 neutralization data and sequence alignment of 181 HIV-1 strains ( 7 ), and using an unbound gp120-core antigen structure as input [PDB:3TGT ( 27 )], all top nine residues predicted by N... P (residues 279–280, 456–461, 466; Figure 2 ) were part of the VRC01 epitope as defined by the gp120/VRC01 complex structure [PDB:3NGB, ( 28 )] (with at least one antigen heavy atom within 5 Å of any antibody heavy atom).
( a ) Predictions from the NEP server, with the top nine residues highlighted in yellow on a structure of the antigen (an unliganded HIV-1 gp120 core, PDB:3TGT).
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