› 5fyj

X-ray diffraction
3.11Å resolution

Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01

Released:
DOI: 10.2210/pdb5fyj/pdb
PDB entry 5fyj coloured by chain, front view.
PDB entry 5fyj coloured by chain, side view.
PDB entry 5fyj coloured by chain, top view.
Source organisms:
Primary publication:
Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G.
Stewart-Jones GB, Soto C, Lemmin T, Chuang GY, Druz A, Kong R, Thomas PV, Wagh K, Zhou T, Behrens AJ, Bylund T, Choi CW, Davison JR, Georgiev IS, Joyce MG, Kwon YD, Pancera M, Taft J, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CC, Wu CY, Bewley CA, Burton DR, Koff WC, Connors M, Crispin M, Baxa U, Korber BT, Wong CH, Mascola JR, Kwong PD
Cell 165 813-26 (2016)
PMID: 27114034

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-207736 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (21 distinct):
Transmembrane protein gp41 Chain: B
Molecule details ›
Chain: B
Length: 161 amino acids
Theoretical weight: 17.99 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: C6ZIG9 (Residues: 510-663; Coverage: 18%)
Gene name: env
Sequence domains: Retroviral envelope protein
35O22 Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
35O22 Chain: E
Molecule details ›
Chain: E
Length: 216 amino acids
Theoretical weight: 23.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: G
Length: 484 amino acids
Theoretical weight: 54.54 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: C6ZIG9 (Residues: 32-506; Coverage: 55%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
PGT122 Chain: H
Molecule details ›
Chain: H
Length: 244 amino acids
Theoretical weight: 26.47 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
PGT122 Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 22.88 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
VRC01 Chains: U, V
Molecule details ›
Chains: U, V
Length: 240 amino acids
Theoretical weight: 26.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
3 bound ligands:
Ligand CIT 3 x CIT
Ligand EDO 2 x EDO
Ligand NAG 3 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P63
Unit cell:
a: 127.16Å b: 127.16Å c: 313.65Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.214 0.273
Expression system: Homo sapiens

Quick links

Citations

54 review citations

The SARS-CoV-2 Spike Glycoprotein Biosynthesis, Structure, Function, and Antigenicity: Implications for the Design of Spike-Based Vaccine Immunogens.
Duan et al. (2020)
53 more

54 mentions without citation

Antibody responses to viral infections: a structural perspective across three different enveloped viruses.
Murin et al. (2019)
53 more