› 6w4m

X-ray diffraction
3.2Å resolution

CRYSTAL STRUCTURE OF THE ADCC-POTENT, WEAKLY NEUTRALIZING HIV ENV CO-RECEPTOR BINDING SITE ANTIBODY N12-I2 FAB IN COMPLEX WITH HIV-1 CLADE A/E GP120 AND M48U1

Released:
DOI: 10.2210/pdb6w4m/pdb
PDB entry 6w4m coloured by chain, front view.
PDB entry 6w4m coloured by chain, side view.
PDB entry 6w4m coloured by chain, top view.
Source organisms:
Primary publication:
Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site.
Tolbert WD, Sherburn R, Gohain N, Ding S, Flinko R, Orlandi C, Ray K, Finzi A, Lewis GK, Pazgier M
BMC Biol 18 91 (2020)
PMID: 32693837

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-207300 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chain: G
Molecule details ›
Chain: G
Length: 353 amino acids
Theoretical weight: 39.16 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
UniProt:
  • Canonical: A0A0M3KKW9 (Residues: 1-353; Coverage: 100%)
Gene name: HIV-1 Env
Sequence domains: Envelope glycoprotein GP120
ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN Chain: L
Molecule details ›
Chain: L
Length: 215 amino acids
Theoretical weight: 23.44 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
ANTI-HIV ANTIBODY N12-I2 FAB HEAVY CHAIN Chain: H
Molecule details ›
Chain: H
Length: 239 amino acids
Theoretical weight: 25.81 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
M48U1 CD4 MIMETIC PEPTIDE Chain: N
Molecule details ›
Chain: N
Length: 28 amino acids
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NAG 9 x NAG
3 modified residues:
Ligand TYS 2 x TYS
Ligand DPR 1 x DPR
Ligand U2X 1 x U2X

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2, SSRL BEAMLINE BL14-1
Spacegroup: P212121
Unit cell:
a: 52.687Å b: 69.522Å c: 213.468Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.244 0.241 0.301
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

2 review citations

SARS-CoV-2 and Human Immunodeficiency Virus: Pathogen Pincer Attack.
Evans et al. (2021)
1 more

1 mention without citation

Defining rules governing recognition and Fc-mediated effector functions to the HIV-1 co-receptor binding site.
Tolbert et al. (2020)