› 6bf4

X-ray diffraction
2.38Å resolution

Crystal Structure of HIV-1 Clade AE Strain CNE55 gp120 Core in Complex with Neutralizing Antibody VRC-PG05 that Targets the Center of the Silent Face on the Outer Domain of gp120

Released:
DOI: 10.2210/pdb6bf4/pdb
PDB entry 6bf4 coloured by chain, front view.
PDB entry 6bf4 coloured by chain, side view.
PDB entry 6bf4 coloured by chain, top view.
Source organisms:
Primary publication:
A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope.
Zhou T, Zheng A, Baxa U, Chuang GY, Georgiev IS, Kong R, O'Dell S, Shahzad-Ul-Hussan S, Shen CH, Tsybovsky Y, Bailer RT, Gift SK, Louder MK, McKee K, Rawi R, Stevenson CH, Stewart-Jones GBE, Taft JD, Waltari E, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CD, Wu CY, Mullikin JC, Bewley CA, Burton DR, Polonis VR, Shapiro L, Wong CH, Mascola JR, Kwong PD, Wu X
Immunity 48 500-513.e6 (2018)
PMID: 29548671

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-230644 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (10 distinct):
Envelope glycoprotein gp160 Chains: A, G
Molecule details ›
Chains: A, G
Length: 344 amino acids
Theoretical weight: 38.22 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: D7S2G1 (Residues: 43-474; Coverage: 41%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120
VRC-PG05 Fab heavy chain Chains: B, H
Molecule details ›
Chains: B, H
Length: 229 amino acids
Theoretical weight: 24.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
VRC-PG05 Fab light chain Chains: C, L
Molecule details ›
Chains: C, L
Length: 219 amino acids
Theoretical weight: 24.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, MAN
Carbohydrate polymer
3 bound ligands:
Ligand NAG 14 x NAG
Ligand EDO 7 x EDO
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: C2
Unit cell:
a: 231.438Å b: 89.255Å c: 123.407Å
α: 90° β: 119.15° γ: 90°
R-values:
R R work R free
0.194 0.192 0.228
Expression system: Homo sapiens

Quick links

Citations

16 review citations

Recent progress in broadly neutralizing antibodies to HIV.
Sok et al. (2018)
15 more

4 mentions without citation

A Structural Update of Neutralizing Epitopes on the HIV Envelope, a Moving Target.
Parker Miller et al. (2021)
3 more