4JM2 image
Deposition Date 2013-03-13
Release Date 2013-05-29
Last Version Date 2024-11-27
Entry Detail
PDB ID:
4JM2
Title:
Crystal Structure of PGT 135 Fab in Complex with gp120 Core Protein from HIV-1 Strain JR-FL Bound to CD4 and 17b Fab
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.10 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.24
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:PGT 135 Heavy chain
Chain IDs:A
Chain Length:236
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:PGT 135 Light chain
Chain IDs:B
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:17b Light chain
Chain IDs:C
Chain Length:214
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:17b Heavy chain
Chain IDs:D
Chain Length:229
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:gp120
Chain IDs:E
Chain Length:321
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:T-cell surface glycoprotein CD4
Gene (Uniprot):CD4
Chain IDs:F
Chain Length:185
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN E ASN GLYCOSYLATION SITE
Primary Citation
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120.
Nat.Struct.Mol.Biol. 20 796 803 (2013)
PMID: 23708606 DOI: 10.1038/nsmb.2594

Abstact

A substantial proportion of the broadly neutralizing antibodies (bnAbs) identified in certain HIV-infected donors recognize glycan-dependent epitopes on HIV-1 gp120. Here we elucidate how the bnAb PGT 135 binds its Asn332 glycan-dependent epitope from its 3.1-Å crystal structure with gp120, CD4 and Fab 17b. PGT 135 interacts with glycans at Asn332, Asn392 and Asn386, using long CDR loops H1 and H3 to penetrate the glycan shield and access the gp120 protein surface. EM reveals that PGT 135 can accommodate the conformational and chemical diversity of gp120 glycans by altering its angle of engagement. Combined structural studies of PGT 135, PGT 128 and 2G12 show that this Asn332-dependent antigenic region is highly accessible and much more extensive than initially appreciated, which allows for multiple binding modes and varied angles of approach; thereby it represents a supersite of vulnerability for antibody neutralization.

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Primary Citation of related structures