5FYK image
Deposition Date 2016-03-08
Release Date 2016-04-27
Last Version Date 2024-11-13
Entry Detail
PDB ID:
5FYK
Keywords:
Title:
Crystal Structure at 3.7 A Resolution of Fully Glycosylated HIV-1 Clade B JR-FL SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.11 Å
R-Value Free:
0.30
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 63
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:JR-FL, GP41 ENV ECTODOMAIN
Mutations:YES
Chain IDs:A (auth: B)
Chain Length:161
Number of Molecules:1
Biological Source:HUMAN IMMUNODEFICIENCY VIRUS 1
Polymer Type:polypeptide(L)
Molecule:35O22
Chain IDs:B (auth: D)
Chain Length:243
Number of Molecules:1
Biological Source:HOMO SAPIENS
Polymer Type:polypeptide(L)
Molecule:35O22
Chain IDs:C (auth: E)
Chain Length:216
Number of Molecules:1
Biological Source:HOMO SAPIENS
Polymer Type:polypeptide(L)
Molecule:JR-FL, GP120 ENV ECTODOMAIN
Gene (Uniprot):env
Mutations:YES
Chain IDs:D (auth: G)
Chain Length:475
Number of Molecules:1
Biological Source:HUMAN IMMUNODEFICIENCY VIRUS 1
Polymer Type:polypeptide(L)
Molecule:PGT122
Chain IDs:E (auth: H)
Chain Length:244
Number of Molecules:1
Biological Source:HOMO SAPIENS
Polymer Type:polypeptide(L)
Molecule:PGT122
Chain IDs:F (auth: L)
Chain Length:213
Number of Molecules:1
Biological Source:HOMO SAPIENS
Polymer Type:polypeptide(L)
Molecule:VRC01
Mutations:YES
Chain IDs:G (auth: U), H (auth: V)
Chain Length:240
Number of Molecules:2
Biological Source:HOMO SAPIENS
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
ASN A ASN GLYCOSYLATION SITE
Ligand Molecules
Primary Citation

Abstact

The HIV-1-envelope (Env) trimer is covered by a glycan shield of ∼90 N-linked oligosaccharides, which comprises roughly half its mass and is a key component of HIV evasion from humoral immunity. To understand how antibodies can overcome the barriers imposed by the glycan shield, we crystallized fully glycosylated Env trimers from clades A, B, and G, visualizing the shield at 3.4-3.7 Å resolution. These structures reveal the HIV-1-glycan shield to comprise a network of interlocking oligosaccharides, substantially ordered by glycan crowding, that encase the protein component of Env and enable HIV-1 to avoid most antibody-mediated neutralization. The revealed features delineate a taxonomy of N-linked glycan-glycan interactions. Crowded and dispersed glycans are differently ordered, conserved, processed, and recognized by antibody. The structures, along with glycan-array binding and molecular dynamics, reveal a diversity in oligosaccharide affinity and a requirement for accommodating glycans among known broadly neutralizing antibodies that target the glycan-shielded trimer.

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Primary Citation of related structures