› 4nee

X-ray diffraction
2.88Å resolution

crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef

Released:
DOI: 10.2210/pdb4nee/pdb
PDB entry 4nee coloured by chain, front view.
PDB entry 4nee coloured by chain, side view.
PDB entry 4nee coloured by chain, top view.
Source organisms:
Primary publication:
How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4.
Ren X, Park SY, Bonifacino JS, Hurley JH
Elife 3 e01754 (2014)
PMID: 24473078

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-138044 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
AP-2 complex subunit sigma Chains: D, F, I, L
Molecule details ›
Chains: D, F, I, L
Length: 142 amino acids
Theoretical weight: 17.04 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P62744 (Residues: 1-142; Coverage: 100%)
Gene names: Ap17, Ap2s1, Claps2
Sequence domains: Clathrin adaptor complex small chain
Structure domains: Beta-Lactamase
AP-2 complex subunit alpha-2 Chains: A, B, G, J
Molecule details ›
Chains: A, B, G, J
Length: 398 amino acids
Theoretical weight: 44.39 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P18484 (Residues: 1-271, 272-395; Coverage: 42%)
Gene names: Adtab, Ap2a2
Sequence domains: Adaptin N terminal region
Structure domains: Leucine-rich Repeat Variant
C-terminal core protein Chains: C, E, H, K
Molecule details ›
Chains: C, E, H, K
Length: 155 amino acids
Theoretical weight: 17.67 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P04601 (Residues: 63-203; Coverage: 68%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef
Structure domains: Nef Regulatory Factor

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 109.558Å b: 168.034Å c: 200.204Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.219 0.267
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Adaptor protein complexes and intracellular transport.
Park et al. (2014)
10 more

12 mentions without citation

How HIV Nef Proteins Hijack Membrane Traffic To Promote Infection.
Buffalo et al. (2019)
11 more