Citations in PubMed

Primary Citation PubMed: 17301785 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 23

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

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.

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Automated detection of conformational epitopes using phage display Peptide sequences.

(2009) Bioinform Biol Insights 3

PubMed: 20140073 | PubMedCentral: PMC2808184 | DOI: null

Mapping of mAb b12 and mAb 17b epitopes In order to map the conformational epitopes of mAb b12 13 onto the crystal structure of gp120 (PDB id: 2NY7) we selected nineteen 12-mer cysteine looped peptide... .

Publication Year: 2009

Crystal structure of the neutralizing Llama V(HH) D7 and its mode of HIV-1 gp120 interaction.

(2010) PLoS One 5

PubMed: 20463957 | PubMedCentral: PMC2864739 | DOI: 10.1371/journal.pone.0010482

The Cα atoms of the heavy chain variable domains (b12 pdb code 2NY7; F105 pdb code 3HI1; b13 pdb code 3IDX; m18 pdb code 2AJ3) were superimposed and the CDR H2 and H3 are represented in the sa... e orientation.

Publication Year: 2010

Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.

(2010) PLoS Comput Biol 6

PubMed: 20949103 | PubMedCentral: PMC2951345 | DOI: 10.1371/journal.pcbi.1000955

The b12 (magenta) bound structure of gp120 (blue), corresponding to PDB code:2NY7.

For signature positions in the b12 binding surface of gp120, we used the X-ray structure corresponding to the PDB code 2NY7 [35] .

The X-ray structure of b12 (marked in magenta) bound to a liganded gp120 core protein (PDB code: 2NY7) with a monomer gp41 that was homology-modeled based on the NMR structure of SIV post-fusion gp41 conformation [129] .

Publication Year: 2010

Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.

(2010) PLoS Pathog 6

PubMed: 21203482 | PubMedCentral: PMC3009598 | DOI: 10.1371/journal.ppat.1001249

The three possible sets of atomic coordinates that are available as starting points to carry out the automated fitting are the structure reported for unliganded SIV gp120 core (2BF1), the structure of... HIV-1 gp120 from the complex with b12 (2NY7), or the structure of HIV-1 gp120 from the complex with sCD4/17b (1GC1).

Publication Year: 2010

MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries.

(2011) BMC Bioinformatics 12

PubMed: 21609501 | PubMedCentral: PMC3124435 | DOI: 10.1186/1471-2105-12-199

PepSurf was the best performer in cases 1G9M, 1E6J, 3IU3 and 2NY7 but the worst in 1N8Z, 2ADF and 1ZTX, and even failed in 1N8Z*.

Publication Year: 2011

Maturation-induced cloaking of neutralization epitopes on HIV-1 particles.

(2011) PLoS Pathog 7

PubMed: 21931551 | PubMedCentral: PMC3169560 | DOI: 10.1371/journal.ppat.1002234

Antibodies and CD4 proteins The following reagents were obtained through the NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID, NIH: CD4-IgG2 from Progenics Pharmaceuticals; HIV... 1 gp120 mAb 2G12 and HIV-1 gp41 mAbs 5F3, 2F5, and 4E10 from Dr. Hermann Katinger; HIV-1 gp120 mAbs F425 B4e8 and F425 A1g8 from Dr. Marshall Posner and Dr. Lisa Cavacini; HIV-1 gp120 mAb IgG1 b12 from Dr. Dennis Burton and Carlos Barbas; HIV-Ig from NABI and NHLBI; HIV-1 gp120 mAbs 17b and E51 from Dr. James E. Robinson; HIV-1 gp41 mAb 50–69 from Dr. Susan Zolla-Pazner; HIV-1 gp41 mAb IgG1 Z13e1 from Dr. Michael Zwick; sCD4-183 from Pharmacia, Inc. Production and labeling of purified recombinant Fabs Amino acid sequences for Fabs b12 and 4E10 were obtained from the Protein Data Bank (PDB IDs 2NY7 and 2FX7).

Publication Year: 2011

Determination of molecular structures of HIV envelope glycoproteins using cryo-electron tomography and automated sub-tomogram averaging.

(2011) J Vis Exp

PubMed: 22158337 | PubMedCentral: PMC3304575 | DOI: 10.3791/2770

As seen in Figure 3B, by combining the density map for trimeric Env determined using cryo-electron tomography with the crystallographically determined structure for monomeric gp120 (red, derived from ... DB ID, 2NY7), we were able to obtain a working molecular model for the trimeric envelope glycoprotein complex (PDB ID, 3DNN) 9 .

As seen in Figure 4B, when this density map is fitted with coordinates of the gp120 spike protein (red, derived from PDB ID, 2NY7) bound by b12 Fab (white), the relative orientations of the three gp120 cores can be discerned (PDB ID, 3DNL).

Publication Year: 2011

Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.

(2012) PLoS Pathog 8

PubMed: 22807678 | PubMedCentral: PMC3395603 | DOI: 10.1371/journal.ppat.1002797

(a, b) Top and side views, respectively, showing the superposition of VRC01-bound (blue) or b12-bound (orange) Env density maps fitted with the corresponding gp120-VRC01 (PDB ID:3NGB) or gp120-b12 (PD... ID:2NY7) coordinates.

Coordinates (PDB IDs: 3DNN, 3NGB, 3SE8, 2NY7 & 1GC1) were fitted into density maps using the software package UCSF Chimera [34] .

(a) Top view of the molecular coordinates for gp120 bound to VRC01 (gp120 in red, VRC01 in blue, PDB ID: 3NGB) or bound to b12 (gp120 in grey, b12 in orange, PDB ID: 2NY7).

Publication Year: 2012

Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing.

(2012) Front Microbiol 3

PubMed: 22876240 | PubMedCentral: PMC3410596 | DOI: 10.3389/fmicb.2012.00277

(D) Mapping of three of the somatically mutated residues N36, Y59, and W111.1, as per IMGT numbering scheme, from each of the HCDRs are shown as sticks using the complex crystal structure of HIV-1 gp1... 0-b12 (PDB code 2NY7).

Publication Year: 2012

Unique C2V3 sequence in HIV-1 envelope obtained from broadly neutralizing plasma of a slow progressing patient conferred enhanced virus neutralization.

(2012) PLoS One 7

PubMed: 23056416 | PubMedCentral: PMC3463516 | DOI: 10.1371/journal.pone.0046713

Molecular Modeling Structural models of HIV-1 C2V3 regions were produced with SWISS MODEL homology modeling server in project mode [64] , using HIV-1 JRFL gp120 (PDB: 2B4C) [65] , b12 (PDB: 2NY7) [33]... and anti-V3 MAb 3074 (PDB: 3MLZ) (Jiang et al., 2010 [66] crystal structures.

Publication Year: 2012

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).

Publication Year: 2012

Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120.

(2012) PLoS One 7

PubMed: 23300605 | PubMedCentral: PMC3531394 | DOI: 10.1371/journal.pone.0052170

( A–C ) Comparisons of gp120 structures in ( A ) the CD4-bound state (PDB ID: 1G9N) [10] , ( B ) the b12 antibody-bound state (PDB ID: 2NY7) [17] , and ( C ) the F105 antibody-bound state (PDB... ID: 3HI1) [20] .

The gp120 from HXBc2 in the b12 antibody-bound state (PDB ID: 2NY7) and the gp120 in complex with CD4 and 17b antibodies (pdb ID: 1G9M) were used in transition pathway calculations.

Publication Year: 2012

C-terminal tail of human immunodeficiency virus gp41: functionally rich and structurally enigmatic.

(2013) J Gen Virol 94

PubMed: 23079381 | PubMedCentral: PMC3542723 | DOI: 10.1099/vir.0.046508-0

The figure was constructed using the EM Database files EMD-5019 (Env) and EMD-5022 (membrane) ( Liu et al. , 2008 ) and the gp120 co-ordinates from PDB file 2NY7 ( Zhou et al. , 2007 ), with gp120 pos... tioned into the EM density map using the ‘Fit in Map’ tool in UCSF Chimera ( Pettersen et al. , 2004 ).

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 [63] ,1RZK [22] , 2B4C [64] , 2NY7 [65] , 3JWD and 3JWO [66] , and 3LMJ [43]... ) as templates.

Publication Year: 2013

Dynamic electrophoretic fingerprinting of the HIV-1 envelope glycoprotein.

(2013) Retrovirology 10

PubMed: 23514633 | PubMedCentral: PMC3648349 | DOI: 10.1186/1742-4690-10-33

First, we consider the unglycosylated gp120 core structure bound to the antibody b12 (PDB code 2NY7) [ 12 ], a three-dimensional structure of this gp120 core with key regions marked is shown (Figure&#... 02009; 3 A).

( A ) Ribbon and space-filling models of gp120 core construct (PDB code 2NY7).

2NY7 is the crystal structure of the b12 bound gp120 core, and 2NY7 (G) is the same structure with glycan residues added to the surface.

2NY7 is the crystal structure of the b12 bound gp120 core, and 2NY7 (G) is the same structure with glycan residues added to the surface.

All structures have been aligned to the 2NY7 structure (as shown in Figure 3A) to facilitate visual comparison between the different conformations and identification of structural features responsible for changes in the electrostatic surface potential.

Publication Year: 2013

An HIV-1 envelope glycoprotein trimer with an embedded IL-21 domain activates human B cells.

(2013) PLoS One 8

PubMed: 23826263 | PubMedCentral: PMC3691133 | DOI: 10.1371/journal.pone.0067309

The trimeric configuration of gp120 in an unliganded spike was obtained by fitting the b12-bound conformation of HxBC2 core gp120 (PDB ID: 2NY7; [70] ) into the cryoelectron tomography density of unli... anded HIV-1 BaL virus using Chimera [71] , [82] .

Publication Year: 2013

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.

(2013) PLoS One 8

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.

A notable exception is the b12-bound structure of C1a(2NY7), which was more solvent exposed, lacked alpha helical structure and contained beta sheet and 3-helix conformations not seen in other representatives of this region.

Publication Year: 2013

bNAber: database of broadly neutralizing HIV antibodies.

(2014) Nucleic Acids Res 42

PubMed: 24214957 | PubMedCentral: PMC3964981 | DOI: 10.1093/nar/gkt1083

Figure 3 shows an example of POSA structure comparisons of bNAbs complexes PDB:2NY7 and PDB:3U7Y aligned on the antigen structure.

Publication Year: 2014

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

Predicted epitope networks were then visually evaluated through comparison with known epitopes or superimposed upon other gp120 crystal structures (PDB ID: 2NY7) which contained additional interacting... molecules such as the b12 fab and CD4 to evaluate the accuracy of the epitope network prediction.

Correct orientation of trimer subunits was obtained by aligning the Cα backbone of the predicted models with the corresponding chains of the trimer structure (PDB ID: 2NY7).

Publication Year: 2014

Antigenic and 3D structural characterization of soluble X4 and hybrid X4-R5 HIV-1 Env trimers.

(2014) Retrovirology 11

PubMed: 24884925 | PubMedCentral: PMC4048260 | DOI: 10.1186/1742-4690-11-42

Docking of unliganded NL4-3 and NL4-3/ADA gp140 At the mass-corrected threshold, the three protruding masses of both 3D reconstructions resembled an unliganded gp120 molecule in size and overall shape... (see for example pdb-ID 2NY7 [ 45 ]).

Automated fitting of a gp120 X-ray structure (pdb 2NY7) into NL4-3 (grey) and NL4-3/ADA gp140 density maps (cyan), viewed from top (A) and side view (B) .

Publication Year: 2014

PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4281296

An ingredient for Env is modeled from the trimer generated from PDB entry 4nco with the b12 Fab fragment from PDB entry 2ny7, currently stored as HIV1_Env_4nco_0_1_3 in the cellPACK database.

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4338595

As a reference, the binding surfaces of each bNAb on gp120 are shown in green (PDB: 3NGB, 2NY7) 21 , 22 .

Publication Year: 2015

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4522616

The majority of the gp120 structures, including the unbound core structures, belong to this group), (ii) the mAb b12-bound (PDB ID 2NY7), (iii) the mAb F105-bound (PDB ID 3HI1), and (iv) the mAb b13-b... und conformations (PDB ID 3IDX).

Publication Year: 2015