› 6de7

X-ray diffraction
4.12Å resolution

Crystal Structure at 4.3 A Resolution of Glycosylated HIV-1 Clade A BG505 SOSIP.664 Prefusion Env Trimer with Interdomain Stabilization 113C-429GCG in Complex with Broadly Neutralizing Antibodies PGT122 and 35O22

Released:
DOI: 10.2210/pdb6de7/pdb
PDB entry 6de7 coloured by chain, front view.
PDB entry 6de7 coloured by chain, side view.
PDB entry 6de7 coloured by chain, top view.
Source organisms:
Primary publication:
Interdomain Stabilization Impairs CD4 Binding and Improves Immunogenicity of the HIV-1 Envelope Trimer.
Zhang P, Gorman J, Geng H, Liu Q, Lin Y, Tsybovsky Y, Go EP, Dey B, Andine T, Kwon A, Patel M, Gururani D, Uddin F, Guzzo C, Cimbro R, Miao H, McKee K, Chuang GY, Martin L, Sironi F, Malnati MS, Desaire H, Berger EA, Mascola JR, Dolan MA, Kwong PD, Lusso P
Cell Host Microbe 23 832-844.e6 (2018)
PMID: 29902444

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-231688 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (13 distinct):
Transmembrane protein gp41 Chain: B
Molecule details ›
Chain: B
Length: 153 amino acids
Theoretical weight: 17.15 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: P04578 (Residues: 512-664; Coverage: 19%)
Gene name: env
Sequence domains: Retroviral envelope protein
Immunoglobulin heavy constant gamma 1 Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01857 (Residues: 1-105; Coverage: 26%)
Gene name: IGHG1
Sequence domains: Immunoglobulin C1-set domain
35O22 light chain Chain: E
Molecule details ›
Chain: E
Length: 216 amino acids
Theoretical weight: 23.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Transmembrane protein gp41 Chain: G
Molecule details ›
Chain: G
Length: 483 amino acids
Theoretical weight: 54.11 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-425, 426-510; Coverage: 56%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
Immunoglobulin heavy constant gamma 1 Chain: H
Molecule details ›
Chain: H
Length: 235 amino acids
Theoretical weight: 25.43 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P01857 (Residues: 1-103; Coverage: 26%)
Gene name: IGHG1
Sequence domains: Immunoglobulin C1-set domain
Immunoglobulin lambda constant 2 Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 22.88 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P0DOY2 (Residues: 1-106; Coverage: 100%)
Gene name: IGLC2
Sequence domains: Immunoglobulin C1-set domain

Ligands and Environments

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
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
2 bound ligands:
Ligand NAG 6 x NAG
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P63
Unit cell:
a: 128.655Å b: 128.655Å c: 312.918Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.252 0.248 0.258
Expression system: Homo sapiens

Quick links

Citations

10 review citations

Env Exceptionalism: Why Are HIV-1 Env Glycoproteins Atypical Immunogens?
Klasse et al. (2020)
9 more

4 mentions without citation

Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan.
Umotoy et al. (2019)
3 more