Primary Citation PubMed: 14981267
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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.
Publication Year: 2007
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
(2008) Nucleic Acids Res 36
PubMed: 18442995 | PubMedCentral: PMC2447719 | DOI: 10.1093/nar/gkn211
Sequence variability in the alignment was mapped onto the 3D-coordinates of gp120 (chain G of PDB 1RZK).
Publication Year: 2008
R5 clade C SHIV strains with tier 1 or 2 neutralization sensitivity: tools to dissect env evolution and to develop AIDS vaccines in primate models.
(2010) PLoS One 5
PubMed: 20657739 | PubMedCentral: PMC2908149 | DOI: 10.1371/journal.pone.0011689
(B) Molecular modeling of SHIV-1157ipEL-p and SHIV-1157ipd3N4 sequences was performed using the X-ray structure of the CD4-bound YU2 gp120 core  ; PDB code 1RZK).
Protein modeling and energy calculations were performed using Discovery Studio (Accelrys Software, Inc.) based on a sequence alignment with the core structure corresponding to the X-ray structure of YU2  (pdb code 1RZK).
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
g008 Figure 8 The four signature sites in the CCR5 CoR region shown in a crystallographic three-dimensional structure of gp120 complexed with CD4 and the CD4i-specific mAb 17b (PDB code: 1RZK).
( A ) b12 signature sites in a three-dimensional structure of gp120 (PDB code: 1RZK) with V1, V2 and V3 loops modeled for visualization as described previously  .
Finally, for spatial mapping of the signature positions in the CD4i region, we used the X-ray structure with a PDB code, 1RZK,  that was solved with a CD4-17b complex.
Systematic protein-protein docking and molecular dynamics studies of HIV-1 gp120 and CD4: insights for new drug development.
(2011) Daru 19
PubMed: 23008694 | PubMedCentral: PMC3436085 | DOI: null
Table 1 Root Mean Square Deviations (RMSDs) of the minimized structures with respect to the initial crystal structure for 1rzk and 1g9n protein complexes with their respective amino acid mutants as ca... culated by Swiss-PdbViewer.
1rzk and 1g9n are the only structures that do not expose unnatural binding distances due to missing amino acids.
Table 3 Root mean square deviations (RMSDs) of the docked conformations (1-10 for FireDock) for 1rzk and 1g9n protein complexes (directed and blind approaches) with reference to the minimized crystal structures as calculated by Swiss-PdbViewer.
Publication Year: 2011
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
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.
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
To represent a CD4-bound gp120 core, we considered the X-ray structure where gp120 core was crystallized with CD4 and 17B antibody (PDB code 1RZK).
A mechanistic understanding of allosteric immune escape pathways in the HIV-1 envelope glycoprotein.
(2013) PLoS Comput Biol 9
PubMed: 23696718 | PubMedCentral: PMC3656115 | DOI: 10.1371/journal.pcbi.1003046
Methods Homology modeling The missing regions of the structures for the YU2, HXB2, and CAP210 sequences (PDB accession numbers 1G9M  , 1RZK  , and 3LQA  ) lacking the V1–V3 loops w... re modeled using the MODELLER program  .
A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies.
PubMed: 24068931 | PubMedCentral: PMC3777863 | DOI: 10.1371/journal.ppat.1003618
The crystal structure of gp120 in complex with sCD4 and 17b (PDB:1RZK;  ) was fitted into the EM density.
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.
Crystal structures of HIV-1 gp120 envelope glycoprotein in complex with NBD analogues that target the CD4-binding site.
(2014) PLoS One 9
PubMed: 24489681 | PubMedCentral: PMC3904841 | DOI: 10.1371/journal.pone.0085940
The structure of YU2core-NBD-557-48d complex was solved by molecular replacement using gp120 structure in complex with CD4 and 17b (PDB ID: 1RZK) as a search model, and structures of other small molec... le bound-clade A/E gp120 93TH057 H375S complexes were solved by molecular replacement using AutoMR in PHENIX software suite  with unliganded clade A/E gp120 core e (PDB ID: 3TGT) as a search model.
Publication Year: 2014
Well-ordered trimeric HIV-1 subtype B and C soluble spike mimetics generated by negative selection display native-like properties.
(2015) PLoS Pathog 11
PubMed: 25569572 | PubMedCentral: PMC4287557 | DOI: 10.1371/journal.ppat.1004570
Model fitting into the EM reconstructions The cryo-EM structure of PGV04-liganded BG505 SOSIP.664 (3J5M), and gp120 with sCD4 (1RZK) were manually fitted into the EM densities and refined by using the... UCSF Chimera  ‘Fit in map’ function.
Publication Year: 2015
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