Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.59 kDa 
• Atom Count: 4018 
• Residue Count: 458 
• Unique protein chains: 2

4KJY

Complex of high-affinity SIRP alpha variant FD6 with CD47

• DOI: 10.2210/pdb4KJY/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-05-04 Released: 2013-06-12 
• Deposition Author(s): Ring, A.M., Ozkan, E., Ho, C.C.M., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.262 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Literature

Engineered SIRP alpha variants as immunotherapeutic adjuvants to anticancer antibodies.

Weiskopf, K., Ring, A.M., Ho, C.C., Volkmer, J.P., Levin, A.M., Volkmer, A.K., Ozkan, E., Fernhoff, N.B., van de Rijn, M., Weissman, I.L., Garcia, K.C.

(2013) Science 341: 88-91

• PubMed: 23722425 
• DOI: 10.1126/science.1238856
• Primary Citation of Related Structures:  
  4KJY


• PubMed Abstract: 
  

CD47 is an antiphagocytic signal that cancer cells employ to inhibit macrophage-mediated destruction. Here, we modified the binding domain of human SIRPα, the receptor for CD47, for use as a CD47 antagonist. We engineered high-affinity SIRPα variants with about a 50,000-fold increased affinity for human CD47 relative to wild-type SIRPα. As high-affinity SIRPα monomers, they potently antagonized CD47 on cancer cells but did not induce macrophage phagocytosis on their own. Instead, they exhibited remarkable synergy with all tumor-specific monoclonal antibodies tested by increasing phagocytosis in vitro and enhancing antitumor responses in vivo. This "one-two punch" directs immune responses against tumor cells while lowering the threshold for macrophage activation, thereby providing a universal method for augmenting the efficacy of therapeutic anticancer antibodies.

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Organizational Affiliation: 

Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte surface antigen CD47	A, C	125	Homo sapiens	Mutation(s): 1  Gene Names: CD47, MER6
Find proteins for Q08722 (Homo sapiens) Explore Q08722  Go to UniProtKB:  Q08722
NIH Common Fund Data Resources
PHAROS  Q08722 GTEx  ENSG00000196776

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
High-affinity SIRPa variant FD6	B, D	133	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	A, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A,C	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.262 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.34	α = 90
b = 71.34	β = 90
c = 399.18	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-04 
• Released Date: 2013-06-12 
Deposition Author(s): Ring, A.M., Ozkan, E., Ho, C.C.M., Garcia, K.C.

Revision History 

• Version 1.0: 2013-06-12
  Type: Initial release
  
• Version 1.1: 2013-08-28
  Changes: Database references
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary