4DQO image
Deposition Date 2012-02-16
Release Date 2013-03-06
Last Version Date 2024-10-16
Entry Detail
PDB ID:
4DQO
Keywords:
Title:
Crystal Structure of PG16 Fab in Complex with V1V2 Region from HIV-1 strain ZM109
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.44 Å
R-Value Free:
0.22
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:1FD6-V1V2 scaffold ZM109 HIV-1 strain
Chain IDs:C
Chain Length:124
Number of Molecules:1
Biological Source:Human immunodeficiency virus 1
Polymer Type:polypeptide(L)
Molecule:PG16 Fab Heavy Chain
Chain IDs:A (auth: H)
Chain Length:246
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:PG16 Fab Light Chain
Chain IDs:B (auth: L)
Chain Length:216
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN C ASN GLYCOSYLATION SITE
PCA A GLN PYROGLUTAMIC ACID
TYS A TYR O-SULFO-L-TYROSINE
Primary Citation
Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16.
Nat.Struct.Mol.Biol. 20 804 813 (2013)
PMID: 23708607 DOI: 10.1038/nsmb.2600

Abstact

HIV-1 uses a diverse N-linked-glycan shield to evade recognition by antibody. Select human antibodies, such as the clonally related PG9 and PG16, recognize glycopeptide epitopes in the HIV-1 V1-V2 region and penetrate this shield, but their ability to accommodate diverse glycans is unclear. Here we report the structure of antibody PG16 bound to a scaffolded V1-V2, showing an epitope comprising both high mannose-type and complex-type N-linked glycans. We combined structure, NMR and mutagenesis analyses to characterize glycan recognition by PG9 and PG16. Three PG16-specific residues, arginine, serine and histidine (RSH), were critical for binding sialic acid on complex-type glycans, and introduction of these residues into PG9 produced a chimeric antibody with enhanced HIV-1 neutralization. Although HIV-1-glycan diversity facilitates evasion, antibody somatic diversity can overcome this and can provide clues to guide the design of modified antibodies with enhanced neutralization.

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Primary Citation of related structures