7MYZ image
Entry Detail
PDB ID:
7MYZ
Title:
Structure of the full length 5-TM receptor CD47 bound to Fab B6H12
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-05-22
Release Date:
2021-09-08
Method Details:
Experimental Method:
Resolution:
3.40 Å
R-Value Free:
0.27
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Fusion protein of Leukocyte surface antigen CD47 an Soluble cytochrome b562
Chain IDs:A (auth: C), B (auth: D)
Chain Length:421
Number of Molecules:2
Biological Source:Homo sapiens, Escherichia coli
Polymer Type:polypeptide(L)
Description:B6H12 Fab heavy chain
Chain IDs:C (auth: H), D (auth: I)
Chain Length:220
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:B6H12 Fab light chain
Chain IDs:E (auth: L), F (auth: M)
Chain Length:213
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation
Structure of the human marker of self 5-transmembrane receptor CD47.
Nat Commun 12 5218 5218 (2021)
PMID: 34471125 DOI: 10.1038/s41467-021-25475-w

Abstact

CD47 is the only 5-transmembrane (5-TM) spanning receptor of the immune system. Its extracellular domain (ECD) is a cell surface marker of self that binds SIRPα and inhibits macrophage phagocytosis, and cancer immuno-therapy approaches in clinical trials are focused on blocking CD47/SIRPα interaction. We present the crystal structure of full length CD47 bound to the function-blocking antibody B6H12. CD47 ECD is tethered to the TM domain via a six-residue peptide linker (114RVVSWF119) that forms an extended loop (SWF loop), with the fundamental role of inserting the side chains of W118 and F119 into the core of CD47 extracellular loop region (ECLR). Using hydrogen-deuterium exchange and molecular dynamics simulations we show that CD47's ECLR architecture, comprised of two extracellular loops and the SWF loop, creates a molecular environment stabilizing the ECD for presentation on the cell surface. These findings provide insights into CD47 immune recognition, signaling and therapeutic intervention.

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