› 6aya

X-ray diffraction
2.4Å resolution

Structure of the native full-length HIV-1 capsid protein in complex with Nup153 peptide

Released:
DOI: 10.2210/pdb6aya/pdb
PDB entry 6aya coloured by chain, front view.
PDB entry 6aya coloured by chain, side view.
PDB entry 6aya coloured by chain, top view.
Source organisms:
Primary publication:
Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization.
Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG
Nat Commun 14 5614 (2023)
PMID: 37699872

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146192 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Capsid protein p24 Chain: A
Molecule details ›
Chain: A
Length: 231 amino acids
Theoretical weight: 25.63 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12493 (Residues: 133-363; Coverage: 46%)
Gene name: gag
Sequence domains:
Nuclear pore complex protein Nup153 Chain: B
Molecule details ›
Chain: B
Length: 17 amino acids
Theoretical weight: 1.69 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P49790 (Residues: 1407-1423; Coverage: 1%)
Gene name: NUP153

Ligands and Environments

2 bound ligands:
Ligand IOD 7 x IOD
Ligand CL 2 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P6
Unit cell:
a: 92.544Å b: 92.544Å c: 58.288Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.236 0.234 0.274
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 mentions without citation

Structure, Function, and Interactions of the HIV-1 Capsid Protein.
Rossi et al. (2021)
2 more