4YFL image
Deposition Date 2015-02-25
Release Date 2015-06-03
Last Version Date 2024-10-30
Entry Detail
PDB ID:
4YFL
Keywords:
Title:
Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 1B2530 in complex with HIV-1 clade A/E 93TH057 gp120
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.39 Å
R-Value Free:
0.32
R-Value Work:
0.26
R-Value Observed:
0.27
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Envelope glycoprotein gp160,Envelope glycoprotein gp160,Envelope glycoprotein gp160
Gene (Uniprot):env
Chain IDs:A (auth: G), D (auth: E)
Chain Length:353
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:1B2530 heavy chain
Chain IDs:B (auth: H), E (auth: F)
Chain Length:227
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:1B2530 Light chain
Chain IDs:C (auth: L), F (auth: I)
Chain Length:215
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.

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Protein

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Disease

Primary Citation of related structures