5W4L image
Deposition Date 2017-06-12
Release Date 2017-11-15
Last Version Date 2023-11-15
Entry Detail
PDB ID:
5W4L
Title:
Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.92 Å
R-Value Free:
0.29
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antibody N12-i3 Fab heavy cha
Chain IDs:E (auth: D), K (auth: B)
Chain Length:225
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antibody N12-i3 light chain
Chain IDs:F (auth: E), L (auth: C)
Chain Length:215
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:clade A/E 93TH057 HIV-1 gp120
Gene (Uniprot):HIV-1 Env
Mutagens:H375S
Chain IDs:A (auth: G), G (auth: A)
Chain Length:385
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antibody N5-i5 Fab heavy chai
Chain IDs:C (auth: H), I (auth: F)
Chain Length:226
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Antibody N5-i5 light chain
Chain IDs:D (auth: L), J (auth: I)
Chain Length:217
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:CD4 mimetic peptide M48U1
Chain IDs:B (auth: N), H (auth: M)
Chain Length:28
Number of Molecules:2
Biological Source:synthetic construct
Peptide-like Molecules
PRD_001094
Primary Citation
Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region.
Structure 25 1719 1731.e4 (2017)
PMID: 29056481 DOI: 10.1016/j.str.2017.09.009

Abstact

Antibodies can have an impact on HIV-1 infection in multiple ways, including antibody-dependent cellular cytotoxicity (ADCC), a correlate of protection observed in the RV144 vaccine trial. One of the most potent ADCC-inducing epitopes on HIV-1 Env is recognized by the C11 antibody. Here, we present the crystal structure, at 2.9 Å resolution, of the C11-like antibody N12-i3, in a quaternary complex with the HIV-1 gp120, a CD4-mimicking peptide M48U1, and an A32-like antibody, N5-i5. Antibody N12-i3 recognizes an epitope centered on the N-terminal "eighth strand" of a critical β sandwich, which our analysis indicates to be emblematic of a late-entry state, after the gp120 detachment. In prior entry states, this sandwich comprises only seven strands, with the eighth strand instead pairing with a portion of the gp120 C terminus. The conformational gymnastics of HIV-1 gp120 thus includes altered β-strand pairing, possibly to reduce immunogenicity, although nevertheless still recognized by the human immune system.

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Primary Citation of related structures
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