Citations in PubMed

Primary Citation PubMed: 16790933 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 16

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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The carbohydrate at asparagine 386 on HIV-1 gp120 is not essential for protein folding and function but is involved in immune evasion.

(2008) Retrovirology 5

PubMed: 18237398 | PubMedCentral: PMC2262092 | DOI: 10.1186/1742-4690-5-10

Residues important for b12 binding [23] are indicated in blue and the asparagines which anchor the glycans involved in 2G12 binding [10-12] are indicated in magenta.

Publication Year: 2008

Broadly neutralizing human anti-HIV antibody 2G12 is effective in protection against mucosal SHIV challenge even at low serum neutralizing titers.

(2009) PLoS Pathog 5

PubMed: 19436712 | PubMedCentral: PMC2674935 | DOI: 10.1371/journal.ppat.1000433

Protein Sequences GenBank accession locus for 2G12 is 10M3_H (heavy chain, Fab 2G12 unliganded) and 10M3_L (light chain, Fab 2G12 unliganded).

Publication Year: 2009

Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

(2009) PLoS Pathog 5

PubMed: 19478876 | PubMedCentral: PMC2680979 | DOI: 10.1371/journal.ppat.1000445

Upper left, binding to soluble human CD4 (4-domain; Progenics); upper right, binding to b12; lower left, binding to 17b; lower right, binding to 2G12.

Publication Year: 2009

PubMed ID is not available.

Published in 2009

PubMedCentral: PMC2767830

Methods Crystal structures of 2G12 in complex with the modified D-mannose and D1-arm, and D-fructose were determined to 1.75, 2.85, and 1.95 Å, respectively.

Results The crystal structures of 2G12 in complex with the modified D-mannose and D1-arm revealed the C-6 methyl substitution enhances antigenicity by making additional hydrophobic contacts with the aromatic side chain of TyrL94.

Publication Year: 2009

phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

(2010) J Appl Crystallogr 43

PubMed: 20648263 | PubMedCentral: PMC2906258 | DOI: 10.1107/S0021889810015608

  R work and R free   R work and R free PDB code PDB file header Recomputed with model_vs_data PDB code PDB file header Recomputed with model_vs_data 1gu8 23.0/25.6 23.0/25.7 2g0v 5.1/... .4 18.5/n.a. 1htq 20.4/22.3 20.7/n.a. 2g0x 5.5/5.3 18.5/n.a. 1l2g 27.8/29.7 25.7/28.7 2g0z 5.8/7.0 18.4/n.a. 1mz0 15.0/17.3 14.6/16.7 2g10 4.5/4.9 17.3/n.a. 1n6j 24.3/26.8 28.5/31.2 2g11 5.1/5.7 17.4/n.a. 1ohh 23.2/28.0 21.7/n.a. 2g12 5.3/6.2 17.4/n.a. 1ot6 14.4/16.1 14.6/n.a. 2g14 5.1/5.8 17.3/n.a. 1ot9 13.4/16.1 13.5/n.a. 2g32 23.9/25.8 25.1/27.3 1t3n 26.5/28.6 25.6/28.0 2gn0 18.8/22.2 23.1/25.9 1u0c 21.4/27.7 28.6/n.a. 2gpm n.a./27.0 24.8/33.0 1u0d 21.7/25.7 37.8/38.5 2gq4 n.a./27.0 25.1/28.4 1vjm 25.2/29.8 24.7/29.3 2gq5 n.a./31.8 26.5/31.7 1wte 17.1/22.3 21.2/26.3 2gq6 n.a./29.5 27.4/28.5 1x0i 23.8/28.2 25.2/28.9 2gq7 n.a./31.0 24.8/31.2 1yk0 24.0/28.4 23.5/23.8 2grz 10.6/10.9 56.9/58.8 1yrq 17.1/22.0 22.4/26.0 2j9j 14.2/19.1 15.3/n.a. 1zbl 21.7/25.3 26.0/28.2 2je4 14.3/18.4 21.4/n.a. 1zev 21.8/27.9 29.0/33.1 2ntw 15.3/19.5 14.4/n.a. 1zy8 20.8/27.6 20.9/27.1 2q3m 15.7/21.7 15.7/21.2 2aaz 29.0/30.5 27.8/29.4 2q3o 18.0/23.5 17.9/23.1 2ce2 14.4/16.3 21.8/23.3 2q3p 18.2/22.4 18.1/21.9 2cl6 14.6/18.6 23.8/27.4 2q3u 13.5/17.1 14.3/17.4 2cl7 14.8/17.0 20.3/23.4 2ull 16.5/19.2 50.1/n.a. 2clc 14.9/18.0 23.7/27.0 2vtu 27.2/31.0 30.7/26.6 2cld 14.9/17.6 21.9/24.8 3c5f 22.4/26.3 22.2/26.1 2d6b 18.2/21.3 17.3/n.a. 3cmy 17.2/21.3 22.4/25.1 2e1c 20.6/23.0 31.1/31.4 3cye 19.3/23.1 18.1/22.0 2evw 15.6/23.6 20.9/23.6 406d 26.2/29.4 33.6/35.8 Table 5 Crystal structures solved using neutron data R work and R free as extracted from PDB file header (second column), and as recalculated using phenix.model_vs_data (third column).

Seven entries ( 2g0v , 2g0x , 2g0z , 2g10 , 2g11 , 2g12 , 2g14 ) report R values obtained after difference refinement (Terwilliger & Berendzen, 1995 ▶ ) that reflect the agreement between model differences and data differences.

Publication Year: 2010

A limited number of antibody specificities mediate broad and potent serum neutralization in selected HIV-1 infected individuals.

(2010) PLoS Pathog 6

PubMed: 20700449 | PubMedCentral: PMC2916884 | DOI: 10.1371/journal.ppat.1001028

Notably, the crystal structure of 2G12 complexed with oligomannoses shows that 2G12 primarily recognizes the terminal mannose on the D1 arm of Man 9 GlcNAc 2 [39] .

Publication Year: 2010

Differences in the mannose oligomer specificities of the closely related lectins from Galanthus nivalis and Zea mays strongly determine their eventual anti-HIV activity.

(2011) Retrovirology 8

PubMed: 21314946 | PubMedCentral: PMC3048538 | DOI: 10.1186/1742-4690-8-10

When competition experiments between GNA, GNA maize and 2G12 for binding to gp120 were performed using SPR-analysis, GNA and GNA maize virtually bound independently of each other to gp120, although th... amplitude of GNA decreased somewhat by 24% when gp120 was saturated with GNA maize (Table 7 ).

Table 7 Competition of GNA, GNA maize and 2G12 mAb for binding to HIV-1 gp120 CBA #RU at 2 min post injection additional gp120 binding by the analyte (%) 5 μM GNA 409 ± 7 20 μM GNA maize 111 ± 8 3 μM 2G12 313 ± 48 5 μM GNA + 20 μM GNA maize 38 ± 4 34 ± 1.4 20 μM GNA maize + 5 μM GNA 310 ± 6 76 ± 0.2 3 μM 2G12 + 5 μM GNA 287 ± 5 70 ± 0.0 5 μM GNA + 3 μM 2G12 78 ± 5 25 ± 5.4 3 μM 2G12 + 20 μM GNA maize 93 ± 17 85 ± 21.3 20 μM GNA maize + 3 μM 2G12 277 ± 4 89 ± 14.9 The Manα1,2-man oligomer-specific lectins [i.e. cyanovirin-N [ 39 ], Pradimicin A [ 41 ], Pradimicin S [ 42 ], actinohivin [ 38 ] and the mAb 2G12 [ 40 ]] and manα1,3/α1,6-man-oligomer specific lectins (i.e. GNA and HHA [ 8 ]) have previously been reported to contain potent anti-HIV activity.

Control injections of 15 μM GNA maize (blue), 0.25 μM GNA (green) and 2.5 μM mAb 2G12 (red) are plotted in panel C. Homology modeling of GNA maize Docking experiments performed with MeMan as a ligand suggested that GNA maize readily differs from GNA by the number of active carbohydrate-binding sites (Figure 7 , Panels A and B).

Publication Year: 2011

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 [61] (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 [37] in white.

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

Phages and HIV-1: from display to interplay.

(2012) Int J Mol Sci 13

PubMed: 22606007 | PubMedCentral: PMC3344243 | DOI: 10.3390/ijms13044727

The crystal structure of MAb 2G12 complexed to the synthetic 2G12.1 peptide was compared to structures of 2G12-oligomannose epitopes and revealed that interactions with the Abs were different for the ... wo ligands.

Publication Year: 2012

Cytokinergic IgE Action in Mast Cell Activation.

(2012) Front Immunol 3

PubMed: 22888332 | PubMedCentral: PMC3412263 | DOI: 10.3389/fimmu.2012.00229

(B) V H domain swapping between the anti-HIV Fab 2G12 (pdb: 1OM3; Calarese et al., 2003 ).

Publication Year: 2012

N332-Directed broadly neutralizing antibodies use diverse modes of HIV-1 recognition: inferences from heavy-light chain complementation of function.

(2013) PLoS One 8

PubMed: 23431362 | PubMedCentral: PMC3576407 | DOI: 10.1371/journal.pone.0055701

g005 Figure 5 DFIRE scores of homology modeling of PGT121-137, based on PGT128, PGT121 and 2G12 template structures.

The structures of PGT128 (PDB accession code 3TYG [25] ) and 2G12 (PDB accession code 1OM3 [24] ) were each used as templates for the structure prediction.

Publication Year: 2013

Interaction and inhibition of dengue envelope glycoprotein with mammalian receptor DC-sign, an in-silico approach.

(2013) PLoS One 8

PubMed: 23527139 | PubMedCentral: PMC3601059 | DOI: 10.1371/journal.pone.0059211

To explain how Dengue envelope protein binds with the 2G12 antibodies and avoids their attachment with DC-SIGN, and also how dengue envelope protein bind to DC-SIGN, which mediates cell attachment and... entry, we conducted unrestrained rigid-body docking of DC-SIGN-DEN-E and DEN-E-2G12.

( a ) Den-E-2G12 Complex represented as a ribbon diagram are shown in Cyan and Pink and Green, respectively.

Heavy chain of 2G12 in complex with Den-E deviate from its non-treated pdb crystal by 0.945 Å after docking.

Docking Results of Den-E-2G12 Complex 444.3 A o2 with ten hydrogen bonds and five salt bridges is the buried surface area at the interface of the Den-E-2G12 H chain.

Light chain in dock complex deviate by 1.239 Å from light chain of pdb non minimized crystal of 2G12(3OAU).

Further qualifications including (i) predicted conserved epitopic residue in interaction sites; (ii) residue conservation of the interaction sites; (iii) Participation of the DC-MAN and antibody 2G12-MAN binding residue in selected complexes were implemented in the finally selected docked complexes from the top 100 predictions.

Pair Wise Docking of Den-E-DC-SIGN and Den-E-2G12 Complex The structural interfaces between Dengue envelope and DC-SIGN CRD domain have been described previously by electron microscopy [55] .

Assessment of the Models High resolution X-Ray 3D crystal structure of dengue virus serotype 2 (pdb code: 1OK8), DC-SIGN CRD (pdb code: 1SL4) and Antibody 2G12 (pdb code: 3OAU) were retrieved form pdb database.

Pre-processed the PDB coordinates of dengue envelope glycoprotein (PDB ID: 1OK8); DC-SIGN CRD domain (PDB ID: 1SL4) and Antibody 2G12 (PDB ID: 3OAU) were used prior than docking procedure for energy minimization through AMBER99 force field distributed in MOE 2011.10 software with 0.05 gradient on default parameters.

Publication Year: 2013

Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.

(2013) Nat Struct Mol Biol 20

PubMed: 23708606 | PubMedCentral: PMC3823233 | DOI: 10.1038/nsmb.2594

Figure 5 Supersite of vulnerability centered on the N332 glycan (a) Binding to the N332 glycan on gp120 for PGT 135, 2G12 and PGT 128 is shown with their respective structures superimposed on glycan N... 32.

The structures of 2G12 (PDBID: 1OP5) and PGT 128 (PDBID: 3TYG) were obtained from the PDB.

Publication Year: 2013

The human anti-HIV antibodies 2F5, 2G12, and PG9 differ in their susceptibility to proteolytic degradation: down-regulation of endogenous serine and cysteine proteinase activities could improve antibody production in plant-based expression platforms.

(2014) Biotechnol J 9

PubMed: 24478053 | PubMedCentral: PMC4162989 | DOI: 10.1002/biot.201300207

Furthermore, 2G12 contains a particularly adaptable linker region between the V H and C H 1 domains, which adopts a buried conformation as compared to a 2G12 variant with a canonical tertiary structur... [ 35 ].

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4373910

The 2G12 Fab footprint is colored within 8 Å of the docked Fab structure because it binds to the tips of several high mannose glycans that are not resolved in the low-resolution model.

Publication Year: 2015