› 6uri

X-ray diffraction
3Å resolution

HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex

Released:
DOI: 10.2210/pdb6uri/pdb
PDB entry 6uri coloured by chain, front view.
PDB entry 6uri coloured by chain, side view.
PDB entry 6uri coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of CD4 downregulation by HIV-1 Nef.
Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X
Nat Struct Mol Biol 27 822-828 (2020)
PMID: 32719457

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-134524 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
AP-2 complex subunit alpha-2 Chain: A
Molecule details ›
Chain: A
Length: 641 amino acids
Theoretical weight: 72.07 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P18484 (Residues: 1-271, 272-620; Coverage: 66%)
Gene names: Adtab, Ap2a2
Sequence domains: Adaptin N terminal region
AP-2 complex subunit sigma Chain: S
Molecule details ›
Chain: S
Length: 142 amino acids
Theoretical weight: 17.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P53680 (Residues: 1-142; Coverage: 100%)
Gene names: AP17, AP2S1, CLAPS2
Sequence domains: Clathrin adaptor complex small chain
Protein Nef Chain: N
Molecule details ›
Chain: N
Length: 186 amino acids
Theoretical weight: 21.03 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P03406 (Residues: 26-206; Coverage: 88%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef
AP-2 complex subunit beta Chain: B
Molecule details ›
Chain: B
Length: 615 amino acids
Theoretical weight: 69.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63010 (Residues: 1-591; Coverage: 63%)
Gene names: ADTB2, AP2B1, CLAPB1
Sequence domains: Adaptin N terminal region
AP-2 complex subunit mu Chain: M
Molecule details ›
Chain: M
Length: 135 amino acids
Theoretical weight: 15.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96CW1 (Residues: 1-135; Coverage: 31%)
Gene names: AP2M1, CLAPM1, KIAA0109
Sequence domains: Clathrin adaptor complex small chain
T-cell surface glycoprotein CD4 Chain: D
Molecule details ›
Chain: D
Length: 62 amino acids
Theoretical weight: 6.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P01730 (Residues: 419-444; Coverage: 6%)
Gene name: CD4
Sequence domains: T cell CD4 receptor C terminal region

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P41
Unit cell:
a: 109.154Å b: 109.154Å c: 178.915Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.241 0.277
Expression system: Escherichia coli

Quick links

Citations

5 review citations

From Entry to Egress: Strategic Exploitation of the Cellular Processes by HIV-1.
Ramdas et al. (2020)
4 more

2 mentions without citation

Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes.
Staudt et al. (2020)
1 more