› 6v6w

X-ray diffraction
6.5Å resolution

Crystal structure of antibody 438-B11 DSS mutant (Cys98A-100aA) in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22

Released:
DOI: 10.2210/pdb6v6w/pdb
PDB entry 6v6w coloured by chain, front view.
PDB entry 6v6w coloured by chain, side view.
PDB entry 6v6w coloured by chain, top view.
Source organism: Human immunodeficiency virus 1
Primary publication:
A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite
Kumar S, Ju B, Shapero B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Hou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Y
Sci Adv 6 eabb1328- (2020)

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octadecamer (preferred)
PDBe Complex ID:
PDB-CPX-232148 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (9 distinct):
35O22 Fab Heavy chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 243 amino acids
Theoretical weight: 26.17 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
35O22 Fab Light chain Chains: B, E
Molecule details ›
Chains: B, E
Length: 216 amino acids
Theoretical weight: 23.32 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
Envelope glycoprotein gp160 Chains: C, G
Molecule details ›
Chains: C, G
Length: 485 amino acids
Theoretical weight: 53.74 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S6 (Residues: 30-503; Coverage: 55%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
B11 DSS Fab heavy chain Chains: F, I
Molecule details ›
Chains: F, I
Length: 235 amino acids
Theoretical weight: 25.23 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
B11 Fab light chain Chains: H, J
Molecule details ›
Chains: H, J
Length: 215 amino acids
Theoretical weight: 23.44 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
Transmembrane protein gp41 Chains: K, T
Molecule details ›
Chains: K, T
Length: 140 amino acids
Theoretical weight: 15.7 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S9 (Residues: 511-663; Coverage: 16%)
Gene name: env
Sequence domains: Retroviral envelope protein

Ligands and Environments

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
1 bound ligand:
Ligand NAG 24 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: R3
Unit cell:
a: 148.534Å b: 148.534Å c: 843.554Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.311 0.309 0.355
Expression system: Homo sapiens

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