Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 64.42 kDa 
• Atom Count: 4197 
• Residue Count: 539 
• Unique protein chains: 3

5TZ2

Crystal structure of human CD47 ECD bound to Fab of C47B222

• DOI: 10.2210/pdb5TZ2/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-11-21 Released: 2017-03-15 
• Deposition Author(s): Cardoso, R.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Anti-leukemic activity and tolerability of anti-human CD47 monoclonal antibodies.

Pietsch, E.C., Dong, J., Cardoso, R., Zhang, X., Chin, D., Hawkins, R., Dinh, T., Zhou, M., Strake, B., Feng, P.H., Rocca, M., Santos, C.D., Shan, X., Danet-Desnoyers, G., Shi, F., Kaiser, E., Millar, H.J., Fenton, S., Swanson, R., Nemeth, J.A., Attar, R.M.

(2017) Blood Cancer J 7: e536-e536

• PubMed: 28234345 
• DOI: 10.1038/bcj.2017.7
• Primary Citation of Related Structures:  
  5TZ2, 5TZT, 5TZU


• PubMed Abstract: 
  

CD47, a broadly expressed cell surface protein, inhibits cell phagocytosis via interaction with phagocyte-expressed SIRPα. A variety of hematological malignancies demonstrate elevated CD47 expression, suggesting that CD47 may mediate immune escape. We discovered three unique CD47-SIRPα blocking anti-CD47 monoclonal antibodies (mAbs) with low nano-molar affinity to human and cynomolgus monkey CD47, and no hemagglutination and platelet aggregation activity. To characterize the anti-cancer activity elicited by blocking CD47, the mAbs were cloned into effector function silent and competent Fc backbones. Effector function competent mAbs demonstrated potent activity in vitro and in vivo, while effector function silent mAbs demonstrated minimal activity, indicating that blocking CD47 only leads to a therapeutic effect in the presence of Fc effector function. A non-human primate study revealed that the effector function competent mAb IgG1 C47B222-(CHO) decreased red blood cells (RBC), hematocrit and hemoglobin by >40% at 1 mg/kg, whereas the effector function silent mAb IgG2σ C47B222-(CHO) had minimal impact on RBC indices at 1 and 10 mg/kg. Taken together, our findings suggest that targeting CD47 is an attractive therapeutic anti-cancer approach. However, the anti-cancer activity observed with anti-CD47 mAbs is Fc effector dependent as are the side effects observed on RBC indices.

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Organizational Affiliation: 

Oncology Discovery, Janssen Research and Development, Spring House, PA, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C47B222 Fab Heavy Chain	H	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C47B222 Fab Light Chain	L	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte surface antigen CD47	C	129	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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	A, B	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	L	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.255 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.567	α = 90
b = 72.934	β = 108.97
c = 72.698	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-11-21 
• Released Date: 2017-03-15 
Deposition Author(s): Cardoso, R.M.F.

Revision History 

• Version 1.0: 2017-03-15
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary