Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78.37 kDa 
• Atom Count: 5364 
• Modelled Residue Count: 694 
• Deposited Residue Count: 696 
• Unique protein chains: 2

5IWL

CD47-diabody complex

• DOI: 10.2210/pdb5IWL/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2016-03-22 Released: 2016-06-29 
• Deposition Author(s): Di, W., Jude, K.M., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

CD47-blocking immunotherapies stimulate macrophage-mediated destruction of small-cell lung cancer.

Weiskopf, K., Jahchan, N.S., Schnorr, P.J., Cristea, S., Ring, A.M., Maute, R.L., Volkmer, A.K., Volkmer, J.P., Liu, J., Lim, J.S., Yang, D., Seitz, G., Nguyen, T., Wu, D., Jude, K., Guerston, H., Barkal, A., Trapani, F., George, J., Poirier, J.T., Gardner, E.E., Miles, L.A., de Stanchina, E., Lofgren, S.M., Vogel, H., Winslow, M.M., Dive, C., Thomas, R.K., Rudin, C.M., van de Rijn, M., Majeti, R., Garcia, K.C., Weissman, I.L., Sage, J.

(2016) J Clin Invest 126: 2610-2620

• PubMed: 27294525 
• DOI: 10.1172/JCI81603
• Primary Citation of Related Structures:  
  5IWL


• PubMed Abstract: 
  

Small-cell lung cancer (SCLC) is a highly aggressive subtype of lung cancer with limited treatment options. CD47 is a cell-surface molecule that promotes immune evasion by engaging signal-regulatory protein alpha (SIRPα), which serves as an inhibitory receptor on macrophages. Here, we found that CD47 is highly expressed on the surface of human SCLC cells; therefore, we investigated CD47-blocking immunotherapies as a potential approach for SCLC treatment. Disruption of the interaction of CD47 with SIRPα using anti-CD47 antibodies induced macrophage-mediated phagocytosis of human SCLC patient cells in culture. In a murine model, administration of CD47-blocking antibodies or targeted inactivation of the Cd47 gene markedly inhibited SCLC tumor growth. Furthermore, using comprehensive antibody arrays, we identified several possible therapeutic targets on the surface of SCLC cells. Antibodies to these targets, including CD56/neural cell adhesion molecule (NCAM), promoted phagocytosis in human SCLC cell lines that was enhanced when combined with CD47-blocking therapies. In light of recent clinical trials for CD47-blocking therapies in cancer treatment, these findings identify disruption of the CD47/SIRPα axis as a potential immunotherapeutic strategy for SCLC. This approach could enable personalized immunotherapeutic regimens in patients with SCLC and other cancers.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5F9 diabody	B [auth A], A [auth B]	234	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte surface antigen CD47	C, D	114	Homo sapiens	Mutation(s): 1  Gene Names: CD47, MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens) Explore Q08722  Go to UniProtKB:  Q08722
PHAROS:  Q08722 GTEx:  ENSG00000196776

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	E [auth C], F [auth C], G [auth C], I [auth D], J [auth D], K [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE	H [auth C], L [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.267 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: P 3₂ 2 1
• Diffraction Data DOI: 10.15785/SBGRID/340 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.28	α = 90
b = 103.28	β = 90
c = 131.13	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2016-03-22 
• Released Date: 2016-06-29 
Deposition Author(s): Di, W., Jude, K.M., Garcia, K.C.

Revision History  

• Version 1.0: 2016-06-29
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 2.0: 2020-02-19
  Changes: Data collection, Database references, Derived calculations, Polymer sequence
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary