› 6z1v

X-ray diffraction
1.33Å resolution

Structure of the EC2 domain of CD9 in complex with nanobody 4E8

Released:
DOI: 10.2210/pdb6z1v/pdb
PDB entry 6z1v coloured by chain, front view.
PDB entry 6z1v coloured by chain, side view.
PDB entry 6z1v 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-210847 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
CD9 antigen Chain: A
Molecule details ›
Chain: A
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 4E8 Chain: B
Molecule details ›
Chain: B
Length: 142 amino acids
Theoretical weight: 15.55 KDa
Source organism: Lama glama
Expression system: Escherichia coli BL21(DE3)

Ligands and Environments

3 bound ligands:
Ligand PGE 1 x PGE
Ligand EDO 1 x EDO
Ligand ACY 1 x ACY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21212
Unit cell:
a: 61.521Å b: 89.446Å c: 35.684Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.153 0.151 0.19
Expression systems:
  • Homo sapiens
  • Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Regulation of ADAM10 by the TspanC8 Family of Tetraspanins and Their Therapeutic Potential.
Harrison et al. (2021)
3 more

3 mentions without citation

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