Primary Citation PubMed: 17901336
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Two HIV-1 variants resistant to small molecule CCR5 inhibitors differ in how they use CCR5 for entry.
(2009) PLoS Pathog 5
PubMed: 19680536 | PubMedCentral: PMC2718843 | DOI: 10.1371/journal.ppat.1000548
pdb; red) or template 2 (2QAD.
Publication Year: 2009
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).
Publication Year: 2010
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).
Figure 2 Electrostatic clustering analysis of the HIV-1 subtypes, using the year 2009 consensus sequences and structural template derived from the gp120 structure with PDB Code 2QAD .
The PDB codes are 2B4C [ 5 ] and 2QAD [ 6 ], both from subtype B.
The calculations were performed using homology model structures derived from the crystallographic structure of gp120 with PDB Code 2QAD and the HIV-1 subtype consensus sequences available in the year 2009 at the HIV Databases of the Los Alamos National Laboratory (Table 1 ).
Figure 3 Electrostatic clustering analysis of the HIV-1 subtypes, using the year 2009 consensus sequences and structural template derived from the gp120 structure with PDB Code 2QAD .
Figure 4 Charge distribution clustering analysis of the HIV-1 subtypes, from the year 2009 consensus sequences and structural template derived from the gp120 structure with PDB Code 2QAD .
(A) Stick representation of backbone and side chains using the gp120 structure with PDB Code 2QAD .
(B) Ribbon representation of backbone using the structure with PDB Code 2QAD .
Publication Year: 2012
Improving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data.
(2012) Bioinformatics 28
PubMed: 22962486 | PubMedCentral: PMC3436800 | DOI: 10.1093/bioinformatics/bts373
Bound V3 loop with highlighted important positions : This plot shows the V3 loop of the PDB structure 2QAD ( Huang et al. , 2007 ), visualized with BALLView ( Hildebrandt et al. , 2010 ).
Insights into the structure, correlated motions, and electrostatic properties of two HIV-1 gp120 V3 loops.
(2012) PLoS One 7
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.
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 ).
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
(B) V3 structure in a bound conformation (2QAD,  ) with the same sphere representation as in panel (A).
Figure S9 Side-chains of the V3 loop in the unbound (A, structure 2B4C) and bound (B, structure 2QAD) conformation.
We additionally tested the performance of a model based on a different V3 loop structure (Protein Data Bank (PDB) code 2QAD)  and performance of models based on combinations of structure- and sequence-based descriptors.
In the bound conformation of the loop (PDB code 2QAD) CS1 and CS2 are located closer to each other than in the open conformation ( Figure 7B and Figure S9 ).
Publication Year: 2013
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
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)  ,  .
HIV-1 diversity in the envelope glycoproteins: implications for viral entry inhibition.
(2013) Viruses 5
PubMed: 23389465 | PubMedCentral: PMC3640516 | DOI: 10.3390/v5020595
Figure 1 Ribbon diagram of gp120 (pdb 2QAD), bovine rhodopsin (pdb 1F88A) and SIV gp41 (pdb 1QBZ).
Structure and dynamics of the gp120 V3 loop that confers noncompetitive resistance in R5 HIV-1(JR-FL) to maraviroc.
(2013) PLoS One 8
PubMed: 23840315 | PubMedCentral: PMC3695986 | DOI: 10.1371/journal.pone.0065115
For the modeling template, we used the crystal structure of HIV-1 gp120 containing an entire V3 region at a resolution of 3.30 Å (PDB code: 2QAD)  .
Characterization of humoral responses to soluble trimeric HIV gp140 from a clade A Ugandan field isolate.
(2013) J Transl Med 11
PubMed: 23835244 | PubMedCentral: PMC3729709 | DOI: 10.1186/1479-5876-11-165
Conformation of the gp120 context as revealed by the X-ray structure (PDB code 2QAD) was used as a prototype to identify variable and constant regions best bound by antibodies of immunized sera [ 52 ]...
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.
(2013) Retrovirology 10
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.
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
For the second round we used V3 from PDB entry 2qad [ 39 ], based on R5-tropic strain YU2 and complexed with the sulfated antibody 412d.
Publication Year: 2014
PubMed ID is not available.
Published in 2015
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.
Publication Year: 2015
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