› 6mft

X-ray diffraction
2.32Å resolution

Crystal structure of glycosylated 426c HIV-1 gp120 core G459C in complex with glVRC01 A60C heavy chain

Released:
DOI: 10.2210/pdb6mft/pdb
PDB entry 6mft coloured by chain, front view.
PDB entry 6mft coloured by chain, side view.
PDB entry 6mft coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core.
Borst AJ, Weidle CE, Gray MD, Frenz B, Snijder J, Joyce MG, Georgiev IS, Stewart-Jones GB, Kwong PD, McGuire AT, DiMaio F, Stamatatos L, Pancera M, Veesler D
Elife 7 (2018)
PMID: 30403372

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-208003 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Heavy Chain glVRC01 Chains: A, H
Molecule details ›
Chains: A, H
Length: 233 amino acids
Theoretical weight: 25.33 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Light chain glVRC01 Chains: B, L
Molecule details ›
Chains: B, L
Length: 210 amino acids
Theoretical weight: 23.02 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Envelope glycoprotein gp160 Chains: C, G
Molecule details ›
Chains: C, G
Length: 347 amino acids
Theoretical weight: 38.59 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: M4Q8P8 (Residues: 39-479; Coverage: 52%)
Gene name: env
Sequence domains: Envelope glycoprotein GP120

Ligands and Environments

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
4 bound ligands:
Ligand NAG 13 x NAG
Ligand PEG 1 x PEG
Ligand CIT 1 x CIT
Ligand EDO 2 x EDO
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 197.082Å b: 109.003Å c: 103.225Å
α: 90° β: 114.47° γ: 90°
R-values:
R R work R free
0.246 0.244 0.295
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Broadly neutralizing antibodies and vaccine design against HIV-1 infection.
Wang et al. (2020)
3 more

5 mentions without citation

HIV-1 VRC01 Germline-Targeting Immunogens Select Distinct Epitope-Specific B Cell Receptors.
Lin et al. (2020)
4 more