6BF4 image
Deposition Date 2017-10-25
Release Date 2018-03-07
Last Version Date 2024-11-20
Entry Detail
PDB ID:
6BF4
Title:
Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.38 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:HIV-1 clade AE gp120 core
Chain IDs:A, D (auth: G)
Chain Length:344
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:VRC-PG05 Fab heavy chain
Chain IDs:B, E (auth: H)
Chain Length:229
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:VRC-PG05 Fab light chain
Chain IDs:C, F (auth: L)
Chain Length:219
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation

Abstact

Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains. The crystal structure of the antigen-binding fragment of VRC-PG05 in complex with gp120 revealed an epitope comprised primarily of N-linked glycans from N262, N295, and N448 at the silent face center. Somatic hypermutation occurred preferentially at antibody residues that interacted with these glycans, suggesting somatic development of glycan recognition. Resistance to VRC-PG05 in donor #74 involved shifting of glycan-N448 to N446 or mutation of glycan-proximal residue E293. HIV-1 neutralization can thus be achieved at the silent face center by glycan-recognizing antibody; along with other known epitopes, the VRC-PG05 epitope completes coverage by neutralizing antibody of all major exposed regions of the prefusion closed trimer.

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Primary Citation of related structures