› 5tzu

X-ray diffraction
2.1Å resolution

Crystal structure of human CD47 ECD bound to Fab of B6H12.2

Released:
DOI: 10.2210/pdb5tzu/pdb
PDB entry 5tzu coloured by chain, front view.
PDB entry 5tzu coloured by chain, side view.
PDB entry 5tzu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies.
Pietsch EC, Dong J, Cardoso R, Zhang X, Chin D, Hawkins R, Dinh T, Zhou M, Strake B, Feng PH, Rocca M, Santos CD, Shan X, Danet-Desnoyers G, Shi F, Kaiser E, Millar HJ, Fenton S, Swanson R, Nemeth JA, Attar RM
Blood Cancer J 7 e536 (2017)
PMID: 28234345

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211958 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (6 distinct):
Light Chain of Fab B6H12.2 Chain: L
Molecule details ›
Chain: L
Length: 214 amino acids
Theoretical weight: 23.37 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Heavy Chain of Fab B6H12.2 Chain: H
Molecule details ›
Chain: H
Length: 227 amino acids
Theoretical weight: 24.2 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Leukocyte surface antigen CD47 Chain: C
Molecule details ›
Chain: C
Length: 129 amino acids
Theoretical weight: 14.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q08722 (Residues: 19-141; Coverage: 40%)
Gene names: CD47, MER6
Sequence domains: CD47 immunoglobulin-like domain
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
4 bound ligands:
Ligand SO4 2 x SO4
Ligand ACT 3 x ACT
Ligand NAG 2 x NAG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: C2
Unit cell:
a: 161.763Å b: 54.527Å c: 83.494Å
α: 90° β: 95.89° γ: 90°
R-values:
R R work R free
0.179 0.177 0.213
Expression system: Homo sapiens

Quick links

Citations

24 review citations

Advances in Anti-Tumor Treatments Targeting the CD47/SIRPĪ± Axis.
Zhang et al. (2020)
23 more

9 mentions without citation

Structural analysis and binding sites of inhibitors targeting the CD47/SIRPĪ± interaction in anticancer therapy.
Huang et al. (2021)
8 more