› 4en2

X-ray diffraction
2.58Å resolution

HIV-1 Nef in complex with MHC-I cytoplasmic domain and Mu1 adaptin subunit of AP1 adaptor (second domain)

Released:
DOI: 10.2210/pdb4en2/pdb
PDB entry 4en2 coloured by chain, front view.
PDB entry 4en2 coloured by chain, side view.
PDB entry 4en2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of evasion of cellular adaptive immunity by HIV-1 Nef.
Jia X, Singh R, Homann S, Yang H, Guatelli J, Xiong Y
Nat Struct Mol Biol 19 701-6 (2012)
PMID: 22705789

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-137686 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
AP-1 complex subunit mu-1 Chains: A, M
Molecule details ›
Chains: A, M
Length: 266 amino acids
Theoretical weight: 30.61 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P35585 (Residues: 158-423; Coverage: 63%)
Gene names: Ap1m1, Cltnm
Sequence domains: Adaptor complexes medium subunit family
Structure domains: Mu homology domain, subdomain B
Protein Nef Chains: B, C
Molecule details ›
Chains: B, C
Length: 206 amino acids
Theoretical weight: 23.4 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q90VU7 (Residues: 1-206; Coverage: 100%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef
Structure domains: Nef Regulatory Factor
HLA class I histocompatibility antigen, A alpha chain Chains: D, E
Molecule details ›
Chains: D, E
Length: 28 amino acids
Theoretical weight: 2.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04439 (Residues: 338-365; Coverage: 8%)
Gene names: HLA-A, HLAA
Sequence domains: MHC_I C-terminus

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P212121
Unit cell:
a: 88.033Å b: 98.128Å c: 112.74Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.21 0.208 0.258
Expression system: Escherichia coli

Quick links

Citations

18 review citations

Protein sorting at the trans-Golgi network.
Guo et al. (2014)
17 more

21 mentions without citation

Cargo recognition in clathrin-mediated endocytosis.
Traub et al. (2013)
20 more