› 4kjy

X-ray diffraction
1.93Å resolution

Complex of high-affinity SIRP alpha variant FD6 with CD47

Released:
DOI: 10.2210/pdb4kjy/pdb
PDB entry 4kjy coloured by chain, front view.
PDB entry 4kjy coloured by chain, side view.
PDB entry 4kjy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Engineered SIRPα variants as immunotherapeutic adjuvants to anticancer antibodies.
Weiskopf K, Ring AM, Ho CC, Volkmer JP, Levin AM, Volkmer AK, Ozkan E, Fernhoff NB, van de Rijn M, Weissman IL, Garcia KC
Science 341 88-91 (2013)
PMID: 23722425

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-164690 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Leukocyte surface antigen CD47 Chains: A, C
Molecule details ›
Chains: A, C
Length: 125 amino acids
Theoretical weight: 14.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q08722 (Residues: 19-135; Coverage: 38%)
Gene names: CD47, MER6
Sequence domains: CD47 immunoglobulin-like domain
Structure domains: Immunoglobulins
High-affinity SIRPa variant FD6 Chains: B, D
Molecule details ›
Chains: B, D
Length: 133 amino acids
Theoretical weight: 14.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

2 bound ligands:
Ligand SO4 3 x SO4
Ligand NAG 8 x NAG
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P6522
Unit cell:
a: 71.34Å b: 71.34Å c: 399.18Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.221 0.219 0.262
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

114 review citations

New insights into cancer immunoediting and its three component phases--elimination, equilibrium and escape.
Mittal et al. (2014)
113 more

3 mentions without citation

Macrophage checkpoint blockade: results from initial clinical trials, binding analyses, and CD47-SIRPα structure-function.
Jalil et al. (2020)
2 more