Primary Citation PubMed: 20616231
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
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.
Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.
(2012) PLoS Pathog 8
PubMed: 22807678 | PubMedCentral: PMC3395603 | DOI: 10.1371/journal.ppat.1002797
The gp120 chain and sCD4 chains from the 1GC1 structure are shown in red, and yellow, respectively, while the gp120 and VRC01 chains from the 3NGB structure are shown in magenta and green, respectivel... .
(a–c) The gp120 portion of the gp120-VRC01 X-ray coordinates (PBD ID:3NGB) is shown after alignment to gp120 fitted to either the unliganded (a), VRC01-bound (b) or VRC03-bound (c) Env density maps to show the similarity in gp120 conformation in each of these states.
(a, b) Two orthogonal views of the superposition of gp120 polypeptides derived from the complex with sCD4 and 17b (PDB ID: 1GC1) and the complex with VRC01 (PDB ID: 3NGB).
X-ray coordinates for the gp120-VRC01 complex (PDB ID:3NGB) were fitted into the map and subsequently aligned to the gp120-CD4/17b (PDB ID:1GC1) complex.
Coordinates shown are for VRC01-bound gp120 (PDB: 3NGB), with gp120 in red and VRC01 in blue.
By fitting three copies of the X-ray structure of monomeric gp120 with VRC01 Fab (PDB ID: 3NGB) into the map, we obtained a molecular model for the VRC01-bound Env trimer.
The maps are shown with the fits obtained for the VRC01-bound map, fitted with coordinates for gp120-VRC01 Fab (PDB ID:3NGB).
(e, f) Top and side views, respectively, of the VRC01-bound HIV-1 BaL Env density map fitted with X-ray coordinates of the gp120-VRC01 Fab complex (PDB ID:3NGB).
(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 (PDB ID:2NY7) coordinates.
Coordinates (PDB IDs: 3DNN, 3NGB, 3SE8, 2NY7 & 1GC1) were fitted into density maps using the software package UCSF Chimera  .
(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
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).
The N276 glycosylation site is required for HIV-1 neutralization by the CD4 binding site specific HJ16 monoclonal antibody.
(2013) PLoS One 8
PubMed: 23874792 | PubMedCentral: PMC3714269 | DOI: 10.1371/journal.pone.0068863
In blue are shown the footprints of CD4 (pdb accession n° 1gc1) and the CD4bs-specific antibodies PGV04 (pdb n°: 3se9), b12 (pdb n°: 3dnl), and VRC01 (pdb n°: 3ngb).
Structural Analyses The crystal structure coordinates of the different gp120 molecules interacting with sCD4 (pdb 1gc1) or the human CD4bs-specific antibodies PGV04 (pdb 3se9), b12 (pdb 3dnl) and VRC01 (pdb 3ngb) were used to identify the footprint of interaction of each ligand on gp120 within an interaction distance of 5 A°.
Publication Year: 2013
We're sorry, but a portion of the page could not be displayed.
The error has been logged and will be reviewed by the RCSB PDB.
If time permits, please submit a detail description of the issue on our Contact Us page.
We will try our best to quickly address the issue.
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.