› 7ygg

X-ray diffraction
2.76Å resolution

Crystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)

Released:
DOI: 10.2210/pdb7ygg/pdb
PDB entry 7ygg coloured by chain, front view.
PDB entry 7ygg coloured by chain, side view.
PDB entry 7ygg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structure of Human CD47 in Complex with Engineered SIRPĪ±.D1(N80A).
Yu J, Li S, Chen D, Liu D, Guo H, Yang C, Zhang W, Zhang L, Zhao G, Tu X, Peng L, Liu S, Bai X, Song Y, Jiang Z, Zhang R, Tian W
Molecules 27 (2022)
PMID: 36080360

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160234 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Tyrosine-protein phosphatase non-receptor type substrate 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 142 amino acids
Theoretical weight: 15.26 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P78324 (Residues: 31-171; Coverage: 29%)
Gene names: BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP, SIRPA
Sequence domains: Immunoglobulin V-set domain
Leukocyte surface antigen CD47 Chains: C, D
Molecule details ›
Chains: C, D
Length: 125 amino acids
Theoretical weight: 14.25 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q08722 (Residues: 19-135; Coverage: 38%)
Gene names: CD47, MER6
Sequence domains: CD47 immunoglobulin-like domain

Ligands and Environments

2 bound ligands:
Ligand EDO 3 x EDO
Ligand NAG 4 x NAG
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 53.58Å b: 99.64Å c: 138.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.217 0.265
Expression system: Homo sapiens

Quick links

Citations

2 review citations

The landscape overview of CD47-based immunotherapy for hematological malignancies.
Yang et al. (2023)
1 more