Primary Citation PubMed: 16284180
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Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage.
(2007) PLoS Comput Biol 3
PubMed: 17397254 | PubMedCentral: PMC1848001 | DOI: 10.1371/journal.pcbi.0030058
Accession Numbers The PDB ( http://www.pdb.org ) accession number used in this paper is for gp120 (2b4c, chain G).
Figure 2 V3 of gp120 with Residue Labels Labels in the first row are amino acid identifiers and V3 sequence reference numbers (relative to the subtype B consensus sequence of length 35), labels in the second row are PDB file residue numbers in chain G of 2b4c.
Thus, we chose to evaluate two approaches: (1) to use a simple descriptor ( V3SD Cβ ), which approximates the position of all functional side chain atoms by the fixed Cβ positions of the structure 2b4c [ 20 ]; and (2) a descriptor V3SD scwrl , which uses the crystal structure 2b4c [ 20 ] as a rigid backbone template for the V3 loop region and models side chains using SCWRL [ 24 ].
The protein structure of the HIV-1 JR-FL gp120 protein including the V3 loop (Protein Data Bank (PDB) structure 2b4c [ 20 ], based on a CCR5-using JR-FL variant) was retrieved from the RCSB PDB ( http://www.pdb.org ).
Positions 7a, 12a, 12b, 12c, 14a, 14b, 18a, 18b, and 24a are insertions relative to the structure PDB 2b4c as well as the subtype B consensus sequence.
Publication Year: 2007
Search for allosteric disulfide bonds in NMR structures.
(2007) BMC Struct Biol 7
PubMed: 17640393 | PubMedCentral: PMC1949407 | DOI: 10.1186/1472-6807-7-49
2 Eght X-ray structures from PDB IDs 1g9m , 1g9n , 1gcn , 1rzj , 1rzk , 1yy1 , 1yym and 2b4c were used for this analysis from.
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope.
PubMed: 18039027 | PubMedCentral: PMC2082504 | DOI: 10.1371/journal.pcbi.0030231
Accession Number The Research Collaboratory for Structural Bioinformatics Protein Data Bank ( http://www.rcsb.org/ ) accession number for the V3 loop of HIV-1 gp120 complexed to the CD4 receptor and X... antibody is 2B4C.
Mean tertiary distance ( y -axis) was calculated from the structural coordinates of residues in the PDB model 2B4C [ 28 ].
Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS.
(2007) Retrovirology 4
PubMed: 18076768 | PubMedCentral: PMC2225424 | DOI: 10.1186/1742-4690-4-89
Structural modeling Proteins structures of unliganded SIV gp120 (2BF1) [ 66 , 94 ] and the V3 loop-containing protein structure of JR-FL (2B4C) [ 95 ] were obtained from the RCSB Protein Data Bank.
Net positive charge of HIV-1 CRF01_AE V3 sequence regulates viral sensitivity to humoral immunity.
(2008) PLoS One 3
PubMed: 18787705 | PubMedCentral: PMC2527523 | DOI: 10.1371/journal.pone.0003206
As the modelling template, we used the crystal structure of HIV-1 gp120 containing an entire V3 element at a resolution of 3.30Å (PDB code: 2B4C), which represents the structure after the CD4 ... inding  .
Publication Year: 2008
The V1-V3 region of a brain-derived HIV-1 envelope glycoprotein determines macrophage tropism, low CD4 dependence, increased fusogenicity and altered sensitivity to entry inhibitors.
(2008) Retrovirology 5
PubMed: 18837996 | PubMedCentral: PMC2576352 | DOI: 10.1186/1742-4690-5-89
The consensus amino acid of subtype B Env at position 283 is T, and this is the residue found in the HIV-1 JR-FL gp120, whose structure in complex to CD4 and the CCR5 surrogate 17b mAb is shown in Fig... re 8A (2B4C; visualized with Pymol v0.99 [DeLano Scientific]; CD4 is shown in green) [ 95 ].
Swiss PDB Viewer was used to change T283 (A) to N283 (B) in the HIV-1 JR-FL gp120 crystal structure (2B4C) [ 95 ], as previously described [ 53 ]; potential hydrogen bonds are indicated by dotted lines and the estimated distance is shown, suggesting a greater likelihood for formation of a hydrogen bond with Q40 (shown in yellow) in CD4 (green) for N283 than for T283, in the HIV-1 JR-FL gp120 background.
Inducing cross-clade neutralizing antibodies against HIV-1 by immunofocusing.
PubMed: 19081789 | PubMedCentral: PMC2597739 | DOI: 10.1371/journal.pone.0003937
We compared the primary envelope sequence of the structure file (PDB-ID: 2B4C; HIV-1 subtype B strain JR-FL) and SHIV-1157ip.
3DEX analysis  was used to find structural homology between A12.2 (yellow, orange and green) and the surface of gp120 (PDB ID: 2B4C) with the CD4 binding site shown in red and CCR5 coreceptor contact sites in blue.
Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects.
(2009) Retrovirology 6
PubMed: 19146663 | PubMedCentral: PMC2639529 | DOI: 10.1186/1742-4690-6-4
Visualization of the dN/dS score (the posterior mean value derived from the Empirical Bayes approach using Model M8) onto the molecular surface of gp120 (pdb code 2B4C) using a color grade scale.
Publication Year: 2009
Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus.
(2009) PLoS Pathog 5
PubMed: 19424420 | PubMedCentral: PMC2671596 | DOI: 10.1371/journal.ppat.1000418
Schema analysis PDB files detailing the three dimensional structures of both gp120 (PDB ID: 2B4C, determined by X-ray diffraction, resolution of 3.3 Å, 338 amino acids,  ),... and gp41 (PDB ID 1AIK, determined by X-ray diffraction, resolution of 2 Å, 70 amino acids,  ) were obtained from http://www.rcsb.org .
Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.
PubMed: 19478876 | PubMedCentral: PMC2680979 | DOI: 10.1371/journal.ppat.1000445
Materials and Methods Molecular Modeling To design a more optimal V3 truncation, hydrogen bonding at the V3 base was examined in the gp120 core with V3 structure (PDB ID 2B4C).
Two HIV-1 variants resistant to small molecule CCR5 inhibitors differ in how they use CCR5 for entry.
PubMed: 19680536 | PubMedCentral: PMC2718843 | DOI: 10.1371/journal.ppat.1000548
(A) The CC101.19 cl.7 and CC1/85 cl.7 gp120 structures were modelled with Swiss-Model ( http://swissmodel.expasy.org ) using template 1 (2B4C.
Structure activity relationship of dendrimer microbicides with dual action antiviral activity.
(2010) PLoS One 5
PubMed: 20808791 | PubMedCentral: PMC2925893 | DOI: 10.1371/journal.pone.0012309
The crystal structure of JRFL gp120 containing the V3 variable loop and bound to CD4 and the X5 Fab antibody fragment was used as the template for CD4-bound model of the DRNL wild-type gp120 protein (... rotein Data Bank ID: 2B4C)  .
Publication Year: 2010
Generation of neutralizing antibodies and divergence of SIVmac239 in cynomolgus macaques following short-term early antiretroviral therapy.
(2010) PLoS Pathog 6
PubMed: 20824092 | PubMedCentral: PMC2932721 | DOI: 10.1371/journal.ppat.1001084
Structural patterns of SIV evolution A molecular model of the monomeric SIV gp120 was generated using the crystal structure of the HIV-1 gp120 (PDB ID 2B4C) and the SWISS-MODEL protein modeling server...  .
Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity.
(2010) Nat Struct Mol Biol 17
PubMed: 20357769 | PubMedCentral: PMC2949298 | DOI: 10.1038/nsmb.1796
(b) Surface representations of sCD4 from different gp120–sCD4–CD4i-Fab structures (PDB codes: HXBc2–sCD4–17b: 1G9M 5 ; YU2–sCD4–412d: 2QAD 3 ; JR-FL... 013;sCD4–X5: 2B4C 4 ).
(c) Comparison of the CAP210–sCD4–21c structure with structures of sCD4–CD4i-Fab complexes including clade B gp120s (PDB codes 1G9M 5 , 2QAD 3 , 2B4C 4 for HXBc2–sCD4–17b, YU2–sCD4–412d, and JR-FL–sCD4–X5, respectively).
The core CAP210 structure was superimposed with the HXBc2, YU2, and JR-FL structures (PDB codes 1G9M 5 , 2QAD 3 , 2B4C 4 for HXBc2–sCD4–17b, YU2–sCD4–412d, and JR-FL–sCD4–X5, respectively) (top).
Hierarchical kernel mixture models for the prediction of AIDS disease progression using HIV structural gp120 profiles.
(2010) BMC Genomics 11 Suppl 4
PubMed: 21143806 | PubMedCentral: PMC3005921 | DOI: 10.1186/1471-2164-11-S4-S22
During the glycan profiling, the V3 region of our sequence was not included in the analyses, as the template crystal structure (PDB: 2B4C) was not glycosylated in the V3 region.
Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection.
(2011) PLoS One 6
PubMed: 21283793 | PubMedCentral: PMC3024314 | DOI: 10.1371/journal.pone.0014548
Structural models of HIV-1 and HIV-2 C2-V3-C3 were produced with SWISS-MODEL homology modelling server in project mode resorting to Swiss-Pdb Viewer (DeepView) version 4.0, using PDB file 2B4C (from H... V-1 JR-FL gp120) for HIV-1, and PDB file 2BF1 (from SIV gp120) for HIV-2 as templates  ,  ,  ,  .
Publication Year: 2011
Crystal structure of the HIV-2 neutralizing Fab fragment 7C8 with high specificity to the V3 region of gp125.
PubMed: 21541316 | PubMedCentral: PMC3082531 | DOI: 10.1371/journal.pone.0018767
Molecular modeling A molecular model of the HIV-2 gp125 monomer (subtype SBL6669 isy ; GeneBank ID J04498) was generated using the SWISS-MODEL protein modelling server  based on th... published crystal structure of the V3-containing gp120 molecule (PDB ID 2B4C;  ).
Increased sensitivity to broadly neutralizing antibodies of end-stage disease R5 HIV-1 correlates with evolution in Env glycosylation and charge.
PubMed: 21698221 | PubMedCentral: PMC3116816 | DOI: 10.1371/journal.pone.0020135
Molecular modelling of gp120 from chronic- and end-stage R5 viruses A molecular model of the monomeric HIV-1 gp120 was generated based on the crystal structure of the HIV-1 gp120 (PDB ID 2B4C) using t... e SWISS-MODEL protein modeling server  .
Conformational alterations in the CD4 binding cavity of HIV-1 gp120 influencing gp120-CD4 interactions and fusogenicity of HIV-1 envelopes derived from brain and other tissues.
(2011) Retrovirology 8
PubMed: 21635737 | PubMedCentral: PMC3123634 | DOI: 10.1186/1742-4690-8-42
The crystal structure of JRFL gp120 containing the V3 variable loop and bound to CD4 and the X5 Fab antibody fragment was used as the template for CD4-bound models [ 9 ] (Protein Data Bank ID: 2B4C).
The coordinates for gp120 and CD4 were extracted from the 2B4C crystal structure.
The three-dimensional structural similarity between the 2B4C JRFL crystal structure and the 81 predicted structures of the primary gp120 proteins was < 1.0 Å for all the primary gp120 models (data not shown), indicating a high overall degree of structural similarity.
Envelope deglycosylation enhances antigenicity of HIV-1 gp41 epitopes for both broad neutralizing antibodies and their unmutated ancestor antibodies.
(2011) PLoS Pathog 7
PubMed: 21909262 | PubMedCentral: PMC3164629 | DOI: 10.1371/journal.ppat.1002200
In this figure, the gp120 bearing the V3 loop  (PDB 2B4C)] trimer (red) is modeled over the cryo-EM structure (white mesh) (36), and its representative glycans are indicated in blue with those tha... are bound by the antibody 2G12  in white.
Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties.
(2012) BMC Biophys 5
PubMed: 22313935 | PubMedCentral: PMC3295656 | DOI: 10.1186/2046-1682-5-3
Subtype Sequence Charge 123456789012345678901234567890123456 2B4C CTRPNQNTRKSIHIGPGRAFYTTG-EIIGDIRQAHC 3 2QAD CTRPNNNTRKSINIGPGRALYTTG-EIIGDIRQAHC 3 A CTRPNNNTRKSVRIGPGQAFYATG-DIIGDIRQAHC 3 AB CIRPGNN... RTSIRIGPGQTFYATG-DVIGDIRQAHC 2 AE CTRPSNNTRTSITIGPGQVFYRTG-DIIGDIRKAYC 3 AG CTRPNNNTRKSVRIGPGQTFYATG-DIIGDIRQAHC 3 B CTRPNNNTRKSIHIGPGRAFYATG-DIIGDIRQAHC 3 C CTRPNNNTRKSIRIGPGQTFYATG-DIIGDIRQAHC 3 CPX CTRPNNNTRKSIHIGPGQAFYATG-DIIGDIRQAHC 2 D CTRPYNNTRQSTHIGPGQALYTT---IIGDIRQAHC 2 D35 CTRPYNNTRQSTHIGPGQALYTTK-NIIGDIRQAHC 3 F CTRPNNNTRKSIHLGPGQAFYATG-DIIGDIRKAHC 3 G CTRPNNNTRKSIRIGPGQAFYATG-DIIGDIRQAHC 3 H CTRPNNNTRKSIHIGPGQAFYATG-DIIGDIRQAHC 2 J CIRPANNTRKGIHIGPGQVLYATG-EIIGDIRQAHC 2 K CTRPNNNTRKSIHIGPGRAFYATG-DIIGDIRQAHC 3 N CTRPGNNTGGQVQIGPAMTFYNIE-KIVGDIRQAHC 1 O CERPGNNTVQEIKIGP-MAWYSMGLEENNNSRAAYC -1 V3 loop subtype consensus sequences were obtained using the tools available within the Los Alamos National Laboratory Database ([ 23 ]; http://www.hiv.lanl.go v ), except for sequences 2B4C and 2QAD, which are from the crystal structures deposited at the PDB.
The green box highlights sequences that belong to Subtype D, while the orange box highlights the two crystal structural templates (from 2QAD and 2B4C), which belong to subtype B.
The modeled structures were constructed by back-prediction using the crystallographic template structures and their sequences (from 2B4C and 2QAD).
This was alleviated in the crystal structures 2QAD and 2B4C, which contain multi-protein complexes that stabilize gp120 and the V3 loop.
This was made possible with Modeller, by back-predicting structures using the crystallographic template structures from 2B4C and 2QAD.
The symbol * refers to the global prevalence of Subtype B which includes the two crystal structural templates (from 2QAD and 2B4C).
To assess the degree that V3 loop dynamics affect its electrostatic properties, at least using two extreme conformations of the crystal structures, we performed similar clustering analyses for electrostatic potentials and charges, using the 2B4C structure (Additional Files 1 , 2 and 3 ).
(C) Stick representation of backbone and side chains using the gp120 structure with PDB Code 2B4C .
Click here for file Additional File 3 Charge distribution clustering analysis of the HIV-1 subtypes, from the 2009 consensus, using the structure with PDB Code 2B4C as template .
(D) Ribbon representation of backbone using the gp120 structure with PDB Code 2B4C .
The PDB codes are 2B4C [ 5 ] and 2QAD [ 6 ], both from subtype B.
Supplementary Material Additional File 1 Electrostatic potential clustering analysis of the HIV-1 subtypes, from the 2009 consensus, using the structure with PDB Code 2B4C as template .
Click here for file Additional File 2 Electrostatic potential clustering analysis of the HIV-1 subtypes, from the 2009 consensus, using the structure with PDB Code 2B4C as template .
Publication Year: 2012
Lignosulfonic acid exhibits broadly anti-HIV-1 activity--potential as a microbicide candidate for the prevention of HIV-1 sexual transmission.
(2012) PLoS One 7
PubMed: 22558266 | PubMedCentral: PMC3338758 | DOI: 10.1371/journal.pone.0035906
The structures of JR-FL (R5 type) and HXB2 (X4 type) gp120s containing V3 loops were reconstructed using Modeller 9v8 program  according to the template (PDB: 2B4C) and sequence information from H... V Database ( http://www.hiv.lanl.gov/content/index ).
Structural dynamics of HIV-1 envelope Gp120 outer domain with V3 loop.
PubMed: 22624045 | PubMedCentral: PMC3356331 | DOI: 10.1371/journal.pone.0037530
We deleted the structures of the CD4 receptor and the X5 antibody from the 2B4C complex structure to construct the free gp120 outer domain models of HIV-1 LAI V3 recombinant viruses by homology modeli... g.
Figure 3 shows the 3-D distribution of the H(i) scores of individual amino acids plotted on the HIV-1 gp120 crystal structure (PDB code: 2B4C  ), where the green to orange regions were suggested to have more variable amino acids than the blue ones.
The divided sequences were used to calculate the Shannon entropy, H(i)  , within each subpopulation, and the H(i) values were plotted on the 3-D structure of gp120 (PDB code: 2B4C  ).
The H(i) scores were displayed on the 3-D structure of an HIV-1 gp120 (PDB code: 2B4C  ).
We used the crystal structure of HIV-1 gp120 containing an entire V3 region at a resolution of 3.30 Å (PDB code: 2B4C  ) as the modeling template.
HIV p24 as scaffold for presenting conformational HIV Env antigens.
PubMed: 22912852 | PubMedCentral: PMC3422313 | DOI: 10.1371/journal.pone.0043318
The full V3 loop sequence (green) as observed in the gp120 X-ray structure (PDB accession code 2B4C) has been introduced between the H84 and R100 residues and superimposed to the cyclophillin binding ... oop (red).
Materials and Methods Design of the Antigen Constructs Conformation of the complete V3 loop in the gp120 context as revealed by the X-ray structure (PDB code 2B4C)  was used as a prototype to identify grafting site(s) on the scaffold.
In particular, the residues H84 and R100 appear the optimal structural boundaries for inserting the full V3 loop sequence to residue positions that would allow low RMSD superposition and clash-free match with the termini of the V3 loop as observed in the gp120 X-ray structure (PDB accession code 2B4C)  ( Fig. 1B ).
Unique C2V3 sequence in HIV-1 envelope obtained from broadly neutralizing plasma of a slow progressing patient conferred enhanced virus neutralization.
PubMed: 23056416 | PubMedCentral: PMC3463516 | DOI: 10.1371/journal.pone.0046713
B Predicated conformations of LT5.J4b and LT5.J12 Env structures in the background of JRFL gp120 crystal structure (2B4C) after energy minimization.
Molecular Modeling Structural models of HIV-1 C2V3 regions were produced with SWISS MODEL homology modeling server in project mode  , using HIV-1 JRFL gp120 (PDB: 2B4C)  , b12 (PDB: 2NY7)  and anti-V3 MAb 3074 (PDB: 3MLZ) (Jiang et al., 2010  crystal structures.
The model was prepared in UCSF Chimera in the background of JRFL crystal structure (RSCB PDB: 2B4C).
Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops.
PubMed: 23185486 | PubMedCentral: PMC3501474 | DOI: 10.1371/journal.pone.0049925
Specific side chain residues are shown and are color-coded: yellow denotes residues 1 and 35, forming the disulfide bridge; blue denotes residues involved in the glycosylation motif; red denotes resid... es involved in the “11/24/25” rule; green denotes the conserved GPG motif at the tip of the loop; orange denotes residues involved in salt bridges within the present MD simulations, including residue 9 (blue in 2B4C and 2QAD) and residue 25 (red in 2QAD).
Secondary Structure and Hydrogen Bonds The initial crystallographic secondary structure profiles of the two available gp120 crystal structures with intact V3 loop are partly different ( Figure 1 ): 2B4C possesses a short β-hairpin around the tip, while 2QAD possesses a β-hairpin with longer beta strands, extending from residue Thr8 to Ile26 and consequently the 2QAD conformation is thinner than 2B4C.
Examination of the V3 loop crystallographic structures shows that 2B4C is an open structure, whereas 2QAD is a thin structure, at the stem region ( Figure 1 ), implicating the glycan in stabilizing the β-strand of the stem, through either intra- or inter-molecular interactions.
In 2B4C the presence of a phenylalanine residue in position 20, pointing towards the interior of the peptide and interacting with several residues, differentiates the conformation of the peptide within the 19–26 residue moiety which adopts a loop-like local structure; as a result the structural change facilitates Arg9 to form a salt bridge with residue Asp29, probably conflicting with the formation of a β-hairpin as in 2QAD.
In the 2B4C FEL ( Figure 7A ), the structures of the first (global) and second free energy minima basins are somewhat similar; the RMSD between the two most representative structures of the two basins is 3.6 Å.
The two V3 loop peptides will be referred hereafter by their crystallographic PDB code, 2B4C and 2QAD.
The PDB codes are 2B4C  and 2QAD  .
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 ).
Prime-boost immunization of rabbits with HIV-1 gp120 elicits potent neutralization activity against a primary viral isolate.
(2013) PLoS One 8
PubMed: 23326351 | PubMedCentral: PMC3541383 | DOI: 10.1371/journal.pone.0052732
The results of this study are represented visually using a model of the crystal structure of JR-FL gp120 core  , shown here in the absence of bound CD4 and X5 antibody Fab fragment (pdb: 2B4C).
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.
Max Bergmann lecture protein epitope mimetics in the age of structural vaccinology.
(2013) J Pept Sci 19
PubMed: 23349031 | PubMedCentral: PMC3592999 | DOI: 10.1002/psc.2482
Figure 6 Crystal structure (Protein Data Bank 2B4C) of a complex formed by an engineered gp120 HIV-1 glycoprotein with domains from the cellular receptor CD4 and with a mAb Fab fragment [ 124 ].
Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage.
(2013) PLoS Comput Biol 9
PubMed: 23555214 | PubMedCentral: PMC3605109 | DOI: 10.1371/journal.pcbi.1002977
The numbering of V3 residues used in this manuscript is shown on the 2B4C structure.
Structural descriptor The descriptor of the V3 loop was based on the published structure of the V3 loop with PDB  code 2B4C  .
Atoms of the 2B4C V3 loop structure are represented by dots, representative atoms by larger dots.
Figure S9 Side-chains of the V3 loop in the unbound (A, structure 2B4C) and bound (B, structure 2QAD) conformation.
We aligned the sequences in the dataset and the sequence of the V3 loop of the PDB entry 2B4C using ClustalW  obtaining an alignment of length 50.
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
Structural modeling The core FE gp120 model was created using the previously solved structure of truncated gp120 from a clade B HIV-1 isolate, JR-FL (PDB: 2B4C), as a template.
Identification of human immunodeficiency virus type 1 (HIV-1) gp120-binding sites on scavenger receptor cysteine rich 1 (SRCR1) domain of gp340.
(2013) J Biomed Sci 20
PubMed: 23815775 | PubMedCentral: PMC3721995 | DOI: 10.1186/1423-0127-20-44
Automated docking of SRCR1 to monomeric gp120-CD4-X5 complex Docking of SRCR1 to the gp120-CD4-X5 complex (PDB ID: 2B4C) was performed using ZDOCK3.0.1, a rigid-body protein-protein docking software [... 20 ].
Arginine insertion and loss of N-linked glycosylation site in HIV-1 envelope V3 region confer CXCR4-tropism.
(2013) Sci Rep 3
PubMed: 23925152 | PubMedCentral: PMC3737504 | DOI: 10.1038/srep02389
As a modeling template, we used the crystal structure of HIV-1 gp120 containing the entire V3 element (PDB code: 2B4C) 19 .
Mimicking Protein-Protein Interactions through Peptide-Peptide Interactions: HIV-1 gp120 and CXCR4.
(2013) Front Immunol 4
PubMed: 24027570 | PubMedCentral: PMC3760305 | DOI: 10.3389/fimmu.2013.00257
Peptides were designed based on crystal structures of a gp120–CD4 complex (pdb: 2b4c) and CXCR4 (pdb: 3odu), respectively.
HIV-1 envelope glycoprotein resistance to monoclonal antibody 2G12 is subject-specific and context-dependent in macaques and humans.
PubMed: 24040404 | PubMedCentral: PMC3767832 | DOI: 10.1371/journal.pone.0075277
The model was built by homology modeling using the SWISS- MODEL server ( http://swissmodel.expasy.org/ ) based on the structure of the HIV-1 JRFL gp120 core protein complexed with CD4 and the X5 antib... dy (PDB code 2B4C) [ 27 ].
3D modeling A three-dimensional model of monomeric gp120 was built based on the structure of the HIV-1 JRFL gp120 core protein complexed with CD4 and the X5 antibody (PDB code 2B4C) [ 27 ] by homology modeling using the SWISS-MODEL modeling tool ( http://swissmodel.expasy.org/ ) [ 28 – 30 ] and the input sequences of gp120 from SF162.
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
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 P... B 2PQR framework [ 54 ] with protonation states for all residues determined using PROPKA3.0 [ 55 ] program.
V3 peptide is shown with respect to the rest of the gp120 core (PDB: 2B4C).
Modelling binding between CCR5 and CXCR4 receptors and their ligands suggests the surface electrostatic potential of the co-receptor to be a key player in the HIV-1 tropism.
PubMed: 24215935 | PubMedCentral: PMC3833284 | DOI: 10.1186/1742-4690-10-130
There is no structural similarity between endogenous ligands of CCR5 or CXCR4 and the structure of the V3 loop as it is crystallized in PDB entries 2b4c or 2qad.
All sequences of the V3 loop under consideration were modeled onto the structure of the V3 loop extracted from the PDB entry 2b4c by introducing amino acid mutations using FoldX [ 37 ].
Human immunodeficiency virus and heparan sulfate: from attachment to entry inhibition.
PubMed: 24312095 | PubMedCentral: PMC3834540 | DOI: 10.3389/fimmu.2013.00385
(B) Three-dimensional structure of gp120 in the CD4-bound conformation (from pdb:2b4c), showing the inner and outer domains, the V1/V2 loop stem, and the four β strands (CD4 induced bridging s... eet in blue) that together with the V3 loop (in green) contribute to co-receptor selectivity and interaction.
The influence of N-linked glycans on the molecular dynamics of the HIV-1 gp120 V3 loop.
PubMed: 24303005 | PubMedCentral: PMC3841175 | DOI: 10.1371/journal.pone.0080301
In order to allow direct comparison of our work with that of Yokoyama et al.  , who used the crystal structure 2B4C as template, Gly 25 of the V3-loop (protein residue 322 of HXB2) was mutated to ... rginine.
g001 Figure 1 The HIV-1 gp120 (PDB ID: 2B4C) structures used in this study.
These values represent the entire gp120 protein (based on the amino acid sequence of PDB ID: 2B4C) for the non-glycosylated, glycosylated 5-glycans , and glycosylated 295 trajectories.
Methods Data Preparation The crystal structure of the HIV-1 gp120 core including the V3 loop (PDB ID 2B4C  ) was used as the starting structure for the simulations.
Epitope specificity of human immunodeficiency virus-1 antibody dependent cellular cytotoxicity [ADCC] responses.
(2013) Curr HIV Res 11
PubMed: 24191939 | PubMedCentral: PMC3878369 | DOI: null
Model was created by loop modeling of the missing V1/V2 region using the ICM software routines (MolSoft, LaJolla, CA) and gp120 coordinates from crystal structures PDB:3WJO and PDB:2B4C.
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
In this structure stem region is replaced by an unrelated scaffold, but the stem is independently observed to form anti-parallel strands in multiple gp120 X-ray structures (e.g. PDB ID 2B4C).
Publication Year: 2014
Molecular characterization of HIV-1 subtype C gp-120 regions potentially involved in virus adaptive mechanisms.
PubMed: 24788065 | PubMedCentral: PMC4005737 | DOI: 10.1371/journal.pone.0095183
Three-dimensional mapping and contact maps The core structure used for mapping the positive selected residues corresponds to the X-ray structure of CD4-bound JR-FL gp120 (Protein Data Bank [PDB] ID: 2... 4C)  .
A simple structure-based model for the prediction of HIV-1 co-receptor tropism.
(2014) BioData Min 7
PubMed: 25120583 | PubMedCentral: PMC4124776 | DOI: 10.1186/1756-0381-7-14
In our approach, V3 sequences (from the training set as well as sequences from new patients) are first modeled onto the V3 X-ray structure by Huang et al. [ 11 ] (PDB:2b4c).
First the V3 structure from PDB entry 2b4c [ 11 ] was used, based on the R5-tropic strain JR-FL and bound to antibody X5.
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
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.
PDB entries 3JWD  and 2B4C  contain crystal structures of HIV-1 gp120 core in the CD4-bound state.
3JWD, 2B4C, and 3FUS represent sequences of crystal structures with PDB entries 3JWD (chain A), 2B4C (chain G), and 3FUS (chain A), respectively.
Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies.
(2014) Bioinformatics 30
PubMed: 24930144 | PubMedCentral: PMC4173008 | DOI: 10.1093/bioinformatics/btu194
The structure shown is PDB ID: 2B4C.
Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models.
(2013) Virol J 10
PubMed: 24295501 | PubMedCentral: PMC4220805 | DOI: 10.1186/1743-422X-10-347
The surface of the protein (PDB ID: 2B4C) was shaded from dark blue (posterior probability = 0) to red (posterior probability = 1) according to the posterior probabilit... assigned to each amino acid residue.
Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops.
(2014) Sci Rep 4
PubMed: 25395053 | PubMedCentral: PMC4231788 | DOI: 10.1038/srep07025
The locations of V2 and V3′ on gp120 in the trimeric context appear to preclude the possibility of their joint accessibility on a single gp140 protomer, where the tips of V2 and V3 are found u... wards of 60 Å apart, as observed from PDB coordinates 2B4C 50 .
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
Protein structure of the HIV-1 GP120-CD4-Fab 48d complex (PDB: 2B4C, 3U4E) and mapped GP120 peptide-derived inhibitors.
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 first model was built from the gp120 core protein containing the V3 region of PDB ID: 2B4C 66 , which has 75% and 65% sequence identity with clade B (residue range 83–486) and clade C (residue range 83-471) respectively, but it lacks the V1 and V2 regions.
The residues of the gp120 V3 loop ranging from C296 to C331 were extracted from the PDB file 2B4C and edited using Sybyl-X 2.1.1 (Tripos Software Inc, El Cerrito, CA, USA).
The V3 loop was manually docked into CCR5 under constraints as follows: (1) the C-terminus including the tip (residues 308–330) was modeled from the crystal coordinates of V3 in the context of the HIV-1 gp120 core complexed to CD4 and to the X5 antibody (PDB code 2B4C) [ 3 ] and positioned into CCR5 so as to reproduce the H-bonds established between CXCR4 ECL2 and the peptide CVX15 (PDB code 3OE0, [ 78 ]) and to bring the V3 R313 side chain close to the CCR5 E283 carboxylate; (2) the V3 N-terminus (residues 296–307) was modeled from the crystal coordinates of V3 in the context of the HIV-1 gp120 core complexed to CD4 and to the 412d antibody containing two sulfotyrosines (PDB code 2QAD, [ 9 ]) and positioned into CCR5 so as to bring the side chains of N302 and T303 close to CCR5 Y14.
The mapping of the major modularity classes on the 2B4C gp120 structure (B—stereo view) shows a good agreement with secondary and tertiary structure units.
The only major discrepancy is the position of the V3 loop, but it is important to note that 2B4C structure represents the bound conformation of gp120 and the V3 loop in the unbound state seems to be positioned rather where the graph suggests.
The results were mapped onto the common residues involved in the structure 2B4C, which is also based on a Clade B isolate and features the constant core with the V3 loop in receptor and X5 antibody bound conformation.
Interestingly, the apparent discrepancy between the position of V3 in the graph and the 2B4C structure can be explained by the bound conformation of the structure, while the coevolution network registered the strong relation of these residues to the outer domain—contacts V3 probably makes in the free conformation [ 24 – 26 ].
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