› 5w4l

X-ray diffraction
2.92Å resolution

Crystal structure of the non-neutralizing and ADCC-potent C11-like antibody N12-i3 in complex with HIV-1 clade A/E gp120, the CD4 mimetic M48U1, and the antibody N5-i5.

Released:
DOI: 10.2210/pdb5w4l/pdb
PDB entry 5w4l coloured by chain, front view.
PDB entry 5w4l coloured by chain, side view.
PDB entry 5w4l coloured by chain, top view.
Source organisms:
Primary publication:
Targeting the Late Stage of HIV-1 Entry for Antibody-Dependent Cellular Cytotoxicity: Structural Basis for Env Epitopes in the C11 Region.
Tolbert WD, Gohain N, Alsahafi N, Van V, Orlandi C, Ding S, Martin L, Finzi A, Lewis GK, Ray K, Pazgier M
Structure 25 1719-1731.e4 (2017)
PMID: 29056481

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-230537 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Human immunodeficiency virus 1 envelope glycoprotein Gp120 domain-containing protein Chains: A, G
Molecule details ›
Chains: A, G
Length: 385 amino acids
Theoretical weight: 42.85 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Homo sapiens
CD4 mimetic peptide M48U1 Chains: M, N
Molecule details ›
Chains: M, N
Length: 28 amino acids
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided
Antibody N5-i5 Fab heavy chain Chains: F, H
Molecule details ›
Chains: F, H
Length: 226 amino acids
Theoretical weight: 23.79 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Antibody N5-i5 light chain Chains: I, L
Molecule details ›
Chains: I, L
Length: 217 amino acids
Theoretical weight: 22.94 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Antibody N12-i3 Fab heavy chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 225 amino acids
Theoretical weight: 24.17 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Antibody N12-i3 light chain Chains: C, E
Molecule details ›
Chains: C, E
Length: 215 amino acids
Theoretical weight: 23.49 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens

Ligands and Environments

2 bound ligands:
Ligand NAG 21 x NAG
Ligand CL 2 x CL
2 modified residues:
Ligand DPR 2 x DPR
Ligand U2X 2 x U2X

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2
Unit cell:
a: 311.018Å b: 53.291Å c: 223.577Å
α: 90° β: 128.89° γ: 90°
R-values:
R R work R free
0.234 0.231 0.292
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

1 review citation

Deciphering Fc-mediated Antiviral Antibody Functions in Animal Models.
Schmaljohn et al. (2019)
21 other articles

5 mentions without citation

Structural Basis for Epitopes in the gp120 Cluster A Region that Invokes Potent Effector Cell Activity.
Tolbert et al. (2019)
4 more