Primary Citation PubMed: 22113616
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
Allosteric modulation of the HIV-1 gp120-gp41 association site by adjacent gp120 variable region 1 (V1) N-glycans linked to neutralization sensitivity.
(2013) PLoS Pathog 9
PubMed: 23592978 | PubMedCentral: PMC3616969 | DOI: 10.1371/journal.ppat.1003218
Molecular modeling A homology-based model of HIV-1 AD8 V1V2 was generated from PDB entry 3U4E  using the Modeller algorithm  within Discovery Studio, version 3.0 (Accelrys).
Publication Year: 2013
A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization.
(2013) Retrovirology 10
PubMed: 23384254 | PubMedCentral: PMC3648360 | DOI: 10.1186/1742-4690-10-14
The FE V1/V2 domain model was generated similarly using the recently solved structure of the V1/V2 domain from a clade C isolate, CAP4 (PDB: 3U4E) as a template.
Epitope mapping of conformational V2-specific anti-HIV human monoclonal antibodies reveals an immunodominant site in V2.
(2013) PLoS One 8
PubMed: 23923028 | PubMedCentral: PMC3726596 | DOI: 10.1371/journal.pone.0070859
Modeling of SF162 structure A full length V1V2 homology model for SF162 was created by using the template crystal structure of the 1FD6-V1V2-scaffold complexed with Fab PG9 (PDB Code: 3U4E).
Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.
PubMed: 24086607 | PubMedCentral: PMC3784573 | DOI: 10.1371/journal.pone.0075665
Structures with antibodies PG9 (PDB: 3U4E), CH 58 (PDB: 4HPO) and CH 59 (PDB: 4HPY) are shown where tan and gray colors indicate the light and heavy chains of the antibody, respectively.
Estimated secondary structure propensities within V1/V2 region of HIV gp120 are an important global antibody neutralization sensitivity determinant.
(2014) PLoS One 9
PubMed: 24705879 | PubMedCentral: PMC3976368 | DOI: 10.1371/journal.pone.0094002
Beta-strands(shown as block arrows) are assigned according to the X-ray structure (PDB ID 3U4E).
Secondary structure cartoon is shown below the alignment as assigned in the X-ray structure (PDB 3U4E).
Remarkably, the two pronounced peaks of beta-strand propensity correlation corresponded well to the C-terminal parts of adjacent beta-strands (B and C) observed in the available X-ray structures (Protein Data Bank IDs 3U4E and 3U2S).
Structures were visualized from Protein Data Bank entries 3U4E, 4HPO and 4HPY.
Publication Year: 2014
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 PG9 neutralization data and sequence alignment of 174 HIV-1 strains ( 7 ), and using the V1/V2 region of a scaffolded V1/V2 structure [PDB:3U4E ( 30 )] as antigen structure input, all top six... residues predicted by NEP (residues 160, 162–163, 169–171) were part of the PG9 epitope as defined by the scaffolded V1/V2–PG9 complex structure [PDB:3U4E ( 30 )].
( a ) Predictions from the NEP server, with the two top-scoring residues 160 and 169 highlighted in yellow on a structure of the antigen [residue 126–196 of a scaffolded HIV-1 V1/V2 (PDB:3U4E)].
( b ) Crystal structure of a scaffolded HIV-1 gp120 V1/V2 region in complex with PG9 (PDB:3U4E), with the HIV-1 gp120 V1/V2 region in green, the PG9 heavy chain in cyan and the PG9 light chain in magenta.
PubMed ID is not available.
Published in 2015
As a reference, the approximate positions of the Fabs are shown as transparent surfaces (modeled from PDB accession codes 3NGB, 3U4E and 4NCO) 70 , while glycans known to be relevant to the epitopes a... e shown as magenta sticks 2 , 28 , 30 .
Publication Year: 2015
Published in 2014
Prefusion mature closed state Prefusion partially open intermediate Prefusion receptor-bound open intermediate Postfusion gp120 Crystal structure (4TVP) Crystal structure (4TVP) Crystal structure of c... re (3JWD) with modeled V3 (3HI1) and V1V2 (3U4E) Crystal structure of core (3JWD) with modeled V3 (3HI1) and V1V2 (3U4E) V1V2 Native Rotated 6° Rotated to align with bridging sheet Rotated to align with bridging sheet V3 Native Rotated 6° Protruding towards target cell Protruding towards target cell Core Native Rotated 6° Rotated 50° Rotated 50° N+C-term Native Native Unknown Rotated 45° gp41 Crystal structure (4TVP) Crystal structure (4TVP) with modeled α7 Crystal structure (4TVP) with modeled α7 and α6 removed Crystal structure (chimera of 2X7R and 2EZO) α6 Native Disassembling to α7 Disassembled Extended to postfusion HR1 α7 Native Extending Extended with fusion peptide Extended to postfusion HR1 α8 Native Native Native Extended to postfusion HR2 α9 Native Native Native Extended to postfusion HR2 Supplementary Material 1 Acknowledgments We thank colleagues that contributed reagents, carried out clinical protocols, and provided discussions and comments on the manuscript, as detailed in supplementary information.
Protein structure of the HIV-1 GP120-CD4-Fab 48d complex (PDB: 2B4C, 3U4E) and mapped GP120 peptide-derived inhibitors.
(A) Ribbon diagram of the V1/V2 domain is based on the structure (PDB 3U4E) of McLellan et al. [ 20 ].
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.