Primary Citation PubMed: 21835983
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Structural mechanism of trimeric HIV-1 envelope glycoprotein activation.
(2012) PLoS Pathog 8
PubMed: 22807678 | PubMedCentral: PMC3395603 | DOI: 10.1371/journal.ppat.1002797
Coordinates (PDB IDs: 3DNN, 3NGB, 3SE8, 2NY7 & 1GC1) were fitted into density maps using the software package UCSF Chimera  .
Crystallographic studies of the complexes formed between monomeric HIV-1 gp120 and Fab fragments from antibodies b12  , VRC01  or VRC03 (PDB ID:3SE8) have provided important insights into key interactions that underlie antibody recognition of the CD4-binding region of HIV-1 gp120.
We fitted three copies of the gp120-VRC03 coordinates (PDB ID:3SE8) into the density map of trimeric Env bound to VRC03 to derive a molecular model for this complex on the surface of the virus ( Figures 2g, 2h ).
(g, h) Top and side views, respectively, of the VRC03-bound Env density map fitted with X-ray coordinates for gp120-VRC03 Fab (PDB ID:3SE8).
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).
Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy.
(2013) Nat Struct Mol Biol 20
PubMed: 24154805 | PubMedCentral: PMC3917492 | DOI: 10.1038/nsmb.2711
Molecular architecture of HIV-1 Env trimer in “closed” state The density map of the VRC03-Env complex, fitted (using automated procedures 22 ) with three copies of the crystal structur... of VRC03 Fab complexed to the truncated gp120 core (PDB 3SE8 23 ), reveals the overall structural organization of the complex, including the Fab arms ( Figure 1 ).
Three copies of the X-ray structure (PDB 3SE8 23 ) of the complex of the truncated gp120 core (red) with VRC03 Fab (orange), shown as a ribbon representation are fitted into the density map.
(b) Close-up of the fit of the gp120 portion of the 3SE8 coordinates into the map shown in side (left) and top views (right).
(c) Ribbon diagram of the crystal structure of the gp120 portion of the 3SE8 23 coordinates highlighting some of the major secondary structural elements α0 (yellow), α1 (green), α2 (orange) and α5 (gray) and a sheet formed from strands β 12, β 13, and β 22 (magenta) in the crystal structure of gp120 2 .
The map also includes density for the V1V2 loop region, the gp120 N- and C-termini and the gp41 base, which are absent in the 3SE8 crystal structure.
Although it is likely that there will be important differences in conformation between the structure of gp120 in the trimeric state as compared to that seen in 3D crystals that contain monomeric gp120 25 , our density map suggests that at the present resolution of our map, the general features of the structure of the gp120 component of the trimer, at least in the core region, are well described by the 3SE8 crystal structure.
Publication Year: 2013
Tertiary structure-based prediction of conformational B-cell epitopes through B factors.
(2014) Bioinformatics 30
PubMed: 24931993 | PubMedCentral: PMC4058920 | DOI: 10.1093/bioinformatics/btu281
There are six complexes (3SE8, 3SE9, 4LSP, 4LSU, 3NGB and 4JB9) containing this antigen or a mutated one in PDB.
Publication Year: 2014
A complete, multi-level conformational clustering of antibody complementarity-determining regions.
(2014) PeerJ 2
PubMed: 25071986 | PubMedCentral: PMC4103072 | DOI: 10.7717/peerj.456
The C α -trace of a two-leg superposition of residues H65–H73 and H76–H78 of crystal structures 3RPI (in yellow) and 3SE8 (in red), containing an insertion, onto the equivalent... residues of a typical structure without an insertion (here 3MLY, in blue).
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