Primary Citation PubMed: 20080564
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MiniCD4 protein resistance mutations affect binding to the HIV-1 gp120 CD4 binding site and decrease entry efficiency.
(2012) Retrovirology 9
PubMed: 22551420 | PubMedCentral: PMC3408336 | DOI: 10.1186/1742-4690-9-36
In order to show these residues, the coordinates of the pdb accession code [PDB: 3JWD] were used to report the structure of the gp120 core and the CD4 was replaced by the M48 structure found in [PDB: ... I60] based on the gp120 from the subtype B virus YU2 in complex with sCD4 and the mAb 17b.
This drawing was made using PyMOL with coordinates that can be found at pdb accession codes [PDB:2I60] and [PDB:3JWD].
Publication Year: 2012
Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
(2012) Nat Struct Mol Biol 19
PubMed: 22864288 | PubMedCentral: PMC3443289 | DOI: 10.1038/nsmb.2351
( a, b ) The CD4-bound gp120 core structure (PDB ID: 3JWD) 8 can fit into the local Env trimer cryo-EM density identified by segmentation as the gp120 inner domain and outer domain (See Fig. 2 ).
CD4 binding determinant mimicry for HIV vaccine design.
(2012) Front Immunol 3
PubMed: 23251137 | PubMedCentral: PMC3523313 | DOI: 10.3389/fimmu.2012.00383
, 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).
Escape from human immunodeficiency virus type 1 (HIV-1) entry inhibitors.
(2012) Viruses 4
PubMed: 23342377 | PubMedCentral: PMC3528295 | DOI: null
The PDB accession codes that used were 2BF1 ( A ), 3JWD ( B ), 2B4C ( C ), and 2QAD ( D ).
HIV-1 fusion is blocked through binding of GB Virus C E2-derived peptides to the HIV-1 gp41 disulfide loop [corrected].
(2013) PLoS One 8
PubMed: 23349893 | PubMedCentral: PMC3551756 | DOI: 10.1371/journal.pone.0054452
The coordinates for structure presentations were taken from PDB entries 3JWD and 2EZO for gp120 and gp41, respectively.
Publication Year: 2013
Viral escape from neutralizing antibodies in early subtype A HIV-1 infection drives an increase in autologous neutralization breadth.
(2013) PLoS Pathog 9
PubMed: 23468623 | PubMedCentral: PMC3585129 | DOI: 10.1371/journal.ppat.1003173
This simulated gp120 was modeled using all known CD4-bound gp120 structures (Protein Data Bank [PDB] accession numbers 1G9M  ,1RZK  , 2B4C  , 2NY7  , 3JWD and 3JWO  , and 3LMJ ... ) as templates.
Allosteric modulation of the HIV-1 gp120-gp41 association site by adjacent gp120 variable region 1 (V1) N-glycans linked to neutralization sensitivity.
PubMed: 23592978 | PubMedCentral: PMC3616969 | DOI: 10.1371/journal.ppat.1003218
The model, prepared with the UCSF Chimera package  , is based on the crystal structures of the complex formed between HXBc2 gp120 with gp41-interactive region (gp120 residues 31–284, 334&... x02013;501), sCD4 and 48 d Fab (PDB ID 3JWD) and the YU2 gp120 (residues 285–333)-418d Fab-sCD4 complex (PDB ID 2QAD)  ,  .
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
The CD4 bound structure of gp120 with N-and C- terminal regions is used as a template to show the C1a, C5a, C5b peptides in the context of entire gp120 monomer structure (PDB: 3JWD).
Properties of gp120 core structures All gp120 core PDB structure files (1G9M) [ 48 ], 1RZK [ 49 ], 2B4C [ 50 ], 2NY7 [ 51 ], 3JWD [ 52 ], 3JWO [ 52 ], and 3LQA [ 53 ] were prepared at pH=7 using the PDB 2PQR framework [ 54 ] with protonation states for all residues determined using PROPKA3.0 [ 55 ] program.
Predicting HIV-1 broadly neutralizing antibody epitope networks using neutralization titers and a novel computational method.
(2014) BMC Bioinformatics 15
PubMed: 24646213 | PubMedCentral: PMC3999910 | DOI: 10.1186/1471-2105-15-77
Figure S2 : Actual versus Theoretical Structure: PDB ID: 3JWD (actual) and CPH (theoretical) structure models are shown.
The quality of the predicted model was assessed by creating an alignment of the α-Carbon backbones of PDB ID: 3JWD and the prediction using the DaliLite server.
We compared the patch lists derived from the truncated gp120 monomer structure (PDB ID: 3JWD) and those derived from our full length predicted monomer structure (data not shown).
Of the more than 24 x-ray structures in the PDB for gp120, PDB ID: 3JWD was selected as being the one with the most full-length structure.
Publication Year: 2014
Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures.
(2014) PLoS One 9
PubMed: 24936864 | PubMedCentral: PMC4061080 | DOI: 10.1371/journal.pone.0100400
Protein name PDB ID Citation p24 3H4E  gp41 1SZT  gp120 3JWD  Integrase 1K6Y  Nef 4D8D Unpublished Protease 3TKG  RNase 3LP3  RT 3KLF  Simulating recombinants The protein f... lding and secondary structure disruption tests performed here both relied on a permutation test involving the generation of sets of simulated recombinants with precisely the same genetic distances to the parental viruses but with breakpoints in random genome locations.
Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120.
PubMed: 25105502 | PubMedCentral: PMC4126740 | DOI: 10.1371/journal.pone.0104714
3JWD, 2B4C, and 3FUS represent sequences of crystal structures with PDB entries 3JWD (chain A), 2B4C (chain G), and 3FUS (chain A), respectively.
PDB entries 3JWD  and 2B4C  contain crystal structures of HIV-1 gp120 core in the CD4-bound state.
In addition to the core structure, the chain A of 3JWD contains the N- and C-termini but no the V3 loop, and the chain G of 2B4C contains the V3 loop but no the N- and C-termini.
In order to obtain an as complete as possible model in the bound state, we aligned simultaneously the target sequence to the chain G of 2B4C and chain A of 3JWD after a structural alignment between these two templates ( Figure 1A ).
It should be noted that in (B) only the segments of the N-, C-termini from 3JWD (chain A) and of the loop V3 from 2B4C (chain G) were used as templates for building corresponding structural parts of gp120.
The sequence identities between our target sequence and structure templates 2B4C and 3JWD are 99% and 80%, respectively.
OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.
PubMed: 25153121 | PubMedCentral: PMC4143332 | DOI: 10.1371/journal.pone.0105954
Among CD4-binding site-directed antibodies, most antibodies (such as the VRC01 class) structurally mimic the CD4 receptor ( Fig. 7H , PDB 3JWD) by substantial β-strand contacts to the epitope ... sing HCDR2  .
Comparison of the specificities of IgG, IgG-subclass, IgA and IgM reactivities in African and European HIV-infected individuals with an HIV-1 clade C proteome-based array.
(2015) PLoS One 10
PubMed: 25658330 | PubMedCentral: PMC4319756 | DOI: 10.1371/journal.pone.0117204
As input we used the amino acid sequence of isolate ZA.04.04ZASK146 and a 3D model created with PyMOL (Version 1.3 Schrödinger, LLC) and COOT [ 31 ], in which the V3 loop of the gp120 structur... PDB:2B4C was combined with the core, N- and C-termini of the gp120 structure PDB:3JWD.
Publication Year: 2015
PubMed ID is not available.
Published in 2015
D) The effects of 17b binding to sCD4-bound SOSIP.664 trimers are similarly mapped onto the CD4-bound conformation of gp120, as modeled into the trimer structure (PDB: 3JWD) 70 .
Published in 2014
gp120 is shown in ribbon representation in prefusion mature closed (red) and CD4-bound (yellow, PDB ID: 3JWD 22 ) conformation.
Prefusion mature closed state Prefusion partially open intermediate Prefusion receptor-bound open intermediate Postfusion gp120 Crystal structure (4TVP) Crystal structure (4TVP) Crystal structure of core (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.
For further analysis, three dimensional structural models were developed using web based fully automated program SWISS-MODEL 65 , which yields two highly reliable models for both clade B and clade C s... ructures, based on the template structures of PDB ID 2B4C and 3JWD.
The second model was built from the recent structure (PDB ID: 3JWD) of gp120 with gp41 interactive region 67 .
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