› 3ik5

X-ray diffraction
2.05Å resolution

SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80)

Released:
DOI: 10.2210/pdb3ik5/pdb
PDB entry 3ik5 coloured by chain, front view.
PDB entry 3ik5 coloured by chain, side view.
PDB entry 3ik5 coloured by chain, top view.
Source organisms:
Primary publication:
Pseudo-merohedral twinning and noncrystallographic symmetry in orthorhombic crystals of SIVmac239 Nef core domain bound to different-length TCRzeta fragments.
Kim WM, Sigalov AB, Stern LJ
Acta Crystallogr D Biol Crystallogr 66 163-75 (2010)
PMID: 20124696

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149097 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protein Nef Chains: A, C
Molecule details ›
Chains: A, C
Length: 143 amino acids
Theoretical weight: 16.7 KDa
Source organism: Simian immunodeficiency virus - cpz
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P31818 (Residues: 95-235; Coverage: 54%)
Gene name: nef
Sequence domains: Negative factor, (F-Protein) or Nef
Structure domains: Nef Regulatory Factor
T-cell surface glycoprotein CD3 zeta chain Chains: B, D
Molecule details ›
Chains: B, D
Length: 18 amino acids
Theoretical weight: 2.17 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P20963 (Residues: 63-80; Coverage: 13%)
Gene names: CD247, CD3Z, T3Z, TCRZ
Sequence domains: Immunoreceptor tyrosine-based activation motif

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 47.417Å b: 47.421Å c: 183.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.184
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 citation in other articles

Tetherin/BST-2 antagonism by Nef depends on a direct physical interaction between Nef and tetherin, and on clathrin-mediated endocytosis.
Serra-Moreno et al. (2013)
8 more

8 mentions without citation

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