Citations in PubMed

Primary Citation PubMed: 15729334 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 15

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.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ.

(2006) PLoS Pathog 2

PubMed: 16933990 | PubMedCentral: PMC1557830 | DOI: 10.1371/journal.ppat.0020083

The Protein Data Bank ( http://www.rcsb.org/pdb ) accession number for the unliganded SIV gp120 core is PDB 2BF1.

Publication Year: 2006


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.

Publication Year: 2007


Super-resolution biomolecular crystallography with low-resolution data.

(2010) Nature 464

PubMed: 20376006 | PubMedCentral: PMC2859093 | DOI: 10.1038/nature08892

For the unligated SIV gp120 structure 18 (PDB 2bf1) we restricted the DEN network to the main chain and Cβ-atoms of the reference model (HIV gp120-antibody complex at 2.0 Å resolution ... 9 , PDB 2nxz) and to regions of the structure considered reliable predictors of SIV gp120 structure (at least 35.8 % local sequence identity, Supplementary Table 2 ).

In some extreme cases (PDB 1av1, 2vkz, and 2bf1), the Main Chain RMSD of the template to the corresponding low-resolution PDB structure was around 10 Å, in which case structural similarity is likely to be limited and significant improvement is not expected.

Table 2 DEN Refinement Improves Low Resolution Structures in the PDB a R free R free -R work Ramachandran Score PDB Identifier Resolution(Å) Number Residues DEN noDEN Improvement DEN noDEN DEN noDEN Improvement Comments 1av1 4.00 804 0.335 0.336 0.0012 0.07 0.07 0.840 0.872 −0.0314 1isr 4.00 448 0.233 0.237 0.0043 0.07 0.07 0.833 0.833 0.0000 1jl4 4.30 557 0.353 0.354 0.0009 0.12 0.11 0.718 0.705 0.0127 1pgf 4.50 1102 0.284 0.295 0.0108 0.08 0.11 0.856 0.804 0.0519 Small differences throughout 1r5u 4.50 3517 0.334 0.335 0.0003 0.05 0.05 0.714 0.710 0.0046 1xdv 4.10 1517 0.358 0.367 0.0089 0.12 0.11 0.780 0.783 −0.0034 1xxi 4.10 3532 0.407 0.465 0.0582 0.05 0.12 0.842 0.612 0.2301 Large differences (~ 4 A domain motions) 1ye1 4.50 574 0.312 0.350 0.0381 0.08 0.15 0.894 0.705 0.1890 Small differences throughout 1yi5 4.20 1356 0.323 0.336 0.0139 0.07 0.09 0.758 0.709 0.0497 Local differences in several chains 1z9j 4.50 821 0.317 0.331 0.0135 0.07 0.09 0.838 0.762 0.0761 Large differences in chain A (domain motion) 2a62 4.50 319 0.340 0.353 0.0131 0.07 0.09 0.590 0.606 −0.0159 2bf1 4.00 304 0.479 0.492 0.0131 0.12 0.12 0.467 0.507 −0.0400 2i36 4.10 962 0.387 0.401 0.0137 0.02 0.03 0.839 0.687 0.1520 Local difference in chain B 2qag 4.00 702 0.392 0.401 0.0091 0.02 0.02 0.616 0.614 0.0016 2vkz 4.00 10941 0.327 0.337 0.0095 0.05 0.07 0.832 0.762 0.0692 Large differences in subdomain placements 3bbw 4.00 543 0.304 0.334 0.0304 0.01 0.04 0.876 0.776 0.0998 Significant local difference 3crw 4.00 485 0.324 0.338 0.0136 0.09 0.11 0.836 0.777 0.0589 Large difference in one domain (hinge motion) 3dmk 4.19 2127 0.407 0.428 0.0211 0.08 0.11 0.742 0.653 0.0896 Differences throughout, reference model only 50% 3du7 4.10 1839 0.332 0.336 0.0039 0.09 0.09 0.730 0.707 0.0225 Average 4.19 1708 0.345 0.359 0.0146 0.07 0.09 0.768 0.715 0.0535 Minimum 4.00 304 0.233 0.237 0.0003 0.01 0.02 0.467 0.507 −0.0400 Maximum 4.50 10941 0.479 0.492 0.0582 0.12 0.15 0.894 0.872 0.2301 a Nineteen PDB structures were re-refined with and without DEN ( Online Methods ).

Publication Year: 2010


Bioinformatics and molecular modeling in glycobiology.

(2010) Cell Mol Life Sci 67

PubMed: 20364395 | PubMedCentral: PMC2912727 | DOI: 10.1007/s00018-010-0352-4

Complete N -glycans were modeled at 13 glycosylation sites based on the X-ray structure (pdb code 2BF1 [ 229 ]).

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

Of these, the coordinates for monomeric, unliganded SIV gp120 (PDB ID: 2BF1; [5] ) might be considered a natural choice to obtain a molecular interpretation of the unliganded HIV-1 and... SIV Env trimers since these are the only published coordinates for unliganded SIV or HIV-1 gp120.

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


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 [95] , [96] , [97] , [98] .

Publication Year: 2011


Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution.

(2012) Acta Crystallogr D Biol Crystallogr 68

PubMed: 22505258 | PubMedCentral: PMC3322597 | DOI: 10.1107/S0907444911047834

    R free R free R work Ramachandran score PDB entry Resolution () PHENIX PHENIX with reference DEN † PHENIX PHENIX with reference DEN † PHENIX PHENIX with reference D... N † 1av1 ‡ 4.00 0.343 0.342 0.335 0.11 0.08 0.07 0.462 0.898 0.840 1jl4 4.30 0.344 0.320 0.353 0.11 0.08 0.12 0.655 0.803 0.718 1r5u 4.50 0.248 0.245 0.334 0.05 0.04 0.05 0.627 0.896 0.714 1xdv 4.10 0.345 0.348 0.358 0.11 0.11 0.12 0.758 0.833 0.780 1xxi 4.10 0.297 0.278 0.407 0.09 0.06 0.05 0.538 0.958 0.842 1ye1 4.50 0.318 0.289 0.312 0.16 0.12 0.08 0.818 0.975 0.894 1yi5 4.20 0.317 0.284 0.323 0.10 0.06 0.07 0.608 0.944 0.758 1z9j 4.50 0.236 0.229 0.317 0.08 0.07 0.07 0.593 0.952 0.838 2a62 4.50 0.371 0.354 0.340 0.14 0.11 0.07 0.629 0.749 0.590 2bf1 ‡ 4.00 0.421 0.432 0.479 0.07 0.05 0.12 0.480 0.666 0.467 2i36 4.10 0.412 0.403 0.387 0.09 0.06 0.02 0.568 0.889 0.839 2qag 4.00 0.378 0.379 0.392 0.04 0.04 0.02 0.471 0.781 0.616 2vkz ‡ 4.00 0.278 0.272 0.327 0.08 0.07 0.05 0.770 0.969 0.832 3bbw 4.00 0.321 0.305 0.304 0.08 0.05 0.01 0.806 0.942 0.876 3crw 4.00 0.339 0.292 0.324 0.10 0.06 0.09 0.781 0.872 0.836 3dmk 4.19 0.292 0.282 0.407 0.12 0.09 0.08 0.707 0.827 0.742 3du7 4.10 0.304 0.302 0.332 0.10 0.07 0.09 0.553 0.838 0.730 Average 4.18 0.327 0.315 0.355 0.096 0.072 0.069 0.637 0.870 0.760 † Data taken from Table 2 in Schrder et al. (2010 ▶ ).

‡ 1av1 , 2bf1 and 2vkz were included in the DEN test set as controls where the reference homology model has an 10 r.m.s.d. difference from the starting model.

As noted in the DEN study, 1av1 , 2vkz and 2bf1 all have reference models that differ from the starting model by approximately 10 Å r.m.s.d. and were included to test both the limits of the DEN method and whether or not it would have a negative impact in cases of significant difference between the reference and target models.

R free is slightly higher for 2bf1 compared with phenix.refine alone, but visual inspection of both final models reveals no major distortion following refinement with reference-model restraints.

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


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 ).

Publication Year: 2012


Dynamic electrophoretic fingerprinting of the HIV-1 envelope glycoprotein.

(2013) Retrovirology 10

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

Given that the native (unliganded) HIV-1 gp120 monomer remains unresolved, we considered two additional monomer constructs from SIV for comparison with our base structure [ 22 ], the first being the g... 120 core crystal structure (PDB code 2BF1).

2BF1 is the unliganded gp120 core from SIV, and 2BF1 (L) is the same structure with the addition of modeled variable loop regions.

2BF1 is the unliganded gp120 core from SIV, and 2BF1 (L) is the same structure with the addition of modeled variable loop regions.

Publication Year: 2013


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

For the “closed” trimer model we first generated an FE monomer model using the unliganded SIV gp120 structure as a template (PDB: 2BF1).

Publication Year: 2013


Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.

(2014) J Biomol Struct Dyn 32

PubMed: 23527883 | PubMedCentral: PMC3919177 | DOI: 10.1080/07391102.2013.770372

The structural templates for the CD4-bound and unliganded states of gp120 and for the V3 loop were crystal structures with PDB codes 1G9M (chain G) ( Kwong et al., 2000 ), 2BF1 ( Chen et al., 2005 ) 1... E4 ( Vranken, Budesinsky, Fant, Boulez, & Borremans, 1995 ), respectively.

Publication Year: 2014


Evolution of the human immunodeficiency virus type 2 envelope in the first years of infection is associated with the dynamics of the neutralizing antibody response.

(2013) Retrovirology 10

PubMed: 24156513 | PubMedCentral: PMC4016255 | DOI: 10.1186/1742-4690-10-110

Structural models Structural models of the C2-V3-C3 domain in gp125 were produced with SWISS-MODEL homology modelling server in automated mode, using PDB file 2BF1 (SIV) as template [ 73 , 74 ].

Publication Year: 2013


Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops.

(2014) Sci Rep 4

PubMed: 25395053 | PubMedCentral: PMC4231788 | DOI: 10.1038/srep07025

Location of V3 & V4 loops, CD4 binding angles Coordinates of unliganded gp120 (PDB 2BF1, SIV) were docked into the density map, resulting in good agreement (correlation coefficient of 0.79) ( ... ig. 5A–C ).

(A) Side view of gp140 structure with SIV unliganded gp120 X-ray coordinates (PDB: 2BF1) docked.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4411102

Thus, a thorough search for the same listed Simian Immunodeficiency Virus (SIV) with PDB id: 2BF1 [ 23 ] and a resolution of 4.0Å.

Publication Year: 2015