› 6z20

X-ray diffraction
2.68Å resolution

Structure of the EC2 domain of CD9 in complex with nanobody 4C8

Released:
DOI: 10.2210/pdb6z20/pdb
PDB entry 6z20 coloured by chain, front view.
PDB entry 6z20 coloured by chain, side view.
PDB entry 6z20 coloured by chain, top view.
Source organisms:
Primary publication:
Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F.
Oosterheert W, Xenaki KT, Neviani V, Pos W, Doulkeridou S, Manshande J, Pearce NM, Kroon-Batenburg LM, Lutz M, van Bergen En Henegouwen PM, Gros P
Life Sci Alliance 3 (2020)
PMID: 32958604

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-210848 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
CD9 antigen Chains: A, C
Molecule details ›
Chains: A, C
Length: 89 amino acids
Theoretical weight: 10.13 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P21926 (Residues: 114-191; Coverage: 34%)
Gene names: CD9, GIG2, MIC3, TSPAN29
Sequence domains: Tetraspanin family
Nanobody 4C8 Chains: B, D
Molecule details ›
Chains: B, D
Length: 129 amino acids
Theoretical weight: 14.09 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

2 bound ligands:
Ligand GOL 2 x GOL
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: I212121
Unit cell:
a: 75.645Å b: 121.415Å c: 129.249Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.248
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

CD9, a tetraspanin target for cancer therapy?
Lorico et al. (2021)
3 more

2 mentions without citation

Implications for tetraspanin-enriched microdomain assembly based on structures of CD9 with EWI-F.
Oosterheert et al. (2020)
1 more