› 6utk

X-ray diffraction
3.8Å resolution

Crystal structure of 438-B11 Fab in complex with an uncleaved prefusion optimized (UFO) soluble BG505 trimer and Fab 35O22 at 3.80 Angstrom

Released:
DOI: 10.2210/pdb6utk/pdb
PDB entry 6utk coloured by chain, front view.
PDB entry 6utk coloured by chain, side view.
PDB entry 6utk coloured by chain, top view.
Source organisms:
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, Shapiro B, Lin X, Ren L, Zhang L, Li D, Zhou Z, Feng Y, Sou C, Mann CJ, Hao Y, Sarkar A, Jou J, Nunnally C, Hong K, Wang S, Ge X, Su B, Landais E, Sok D, Zwick MB, He L, Zhu J, Wilson IA, Shao Z
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-232147 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (15 distinct):
35O22 Fab Heavy Chain Chain: D
Molecule details ›
Chain: D
Length: 243 amino acids
Theoretical weight: 26.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
35O22 Fab 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
B11 Fab Light Chain Chain: L
Molecule details ›
Chain: L
Length: 213 amino acids
Theoretical weight: 23.21 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Envelope glycoprotein gp160 Chain: G
Molecule details ›
Chain: 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
Transmembrane protein gp41 Chain: T
Molecule details ›
Chain: T
Length: 140 amino acids
Theoretical weight: 15.7 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: Q2N0S9 (Residues: 511-546, 568-663; Coverage: 15%)
Gene name: env
Sequence domains: Retroviral envelope protein
B11 Fab Heavy chain Chain: H
Molecule details ›
Chain: H
Length: 233 amino acids
Theoretical weight: 25.03 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

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
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
Carbohydrate polymer
1 bound ligand:
Ligand NAG 8 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: R32
Unit cell:
a: 247.308Å b: 247.308Å c: 257.612Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.3 0.299 0.317
Expression system: Homo sapiens

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