8ZCA | pdb_00008zca

Crystal structure of human CD47 ECD bound to Fab of Hu1C8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

An anti-CD47 antibody binds to a distinct epitope in a novel metal ion-dependent manner to minimize cross-linking of red blood cells.

Lu, X.Chen, Z.Yi, C.Ling, Z.Ye, J.Chen, K.Cong, Y.Sonam, W.Cheng, S.Wang, R.Zhang, D.Xu, J.Yang, J.Ma, L.Duan, Q.Sun, X.Ding, J.Sun, B.

(2025) J Biological Chem 301: 110420-110420

  • DOI: https://doi.org/10.1016/j.jbc.2025.110420
  • Primary Citation of Related Structures:  
    8ZCA

  • PubMed Abstract: 

    Cluster of differentiation 47 (CD47) is a widely expressed transmembrane protein that plays a crucial role in immune self-recognition. Cancer cells upregulate CD47 expression to promote immune escape through activating the "don't eat me" signal via interactions with signal regulatory protein α (SIRPα) on macrophages. The effectiveness of anti-CD47 antibodies has been demonstrated in multiple tumour models. However, since CD47 is also expressed in human red blood cells (RBCs) and platelets, the clinical application of anti-CD47 antibodies requires careful consideration of blood toxicity. One major obstacle to the clinical application of CD47 antibodies is the haemagglutination caused by RBCs cross-linking. In this study, we generated Hu1C8, a humanized anti-CD47 monoclonal antibody that demonstrated increased selectivity for binding to CD47 on cancer cells and lacked haemagglutination activity. Epitope mapping and the crystal structure of the Hu1C8 Fab-CD47 extracellular domain (ECD) complex revealed that Hu1C8 binds to a distinct epitope of CD47 in a Ca 2+ -dependent manner. The unique recognition and binding mode allowed Hu1C8 to bind CD47 on RBCs with reduced haemagglutination activity while still maintaining effective antitumour activity. These findings demonstrate a feasible strategy for developing CD47 antibodies with high antitumor activity but low RBC haemagglutination activity. Our study elucidates how epitope-specific antibody influences antibody-induced cell cross-linking, offering innovative strategies for antibody design to either leverage or avoid cell cross-linking effects.


  • Organizational Affiliation
    • Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1C8 Fab light chainA,
C [auth B]
218Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1C8 Fab heavy chainB [auth D],
D [auth C]
225Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Leukocyte surface antigen CD47
E, F
131Homo sapiensMutation(s): 0 
Gene Names: CD47MER6
UniProt & NIH Common Fund Data Resources
Find proteins for Q08722 (Homo sapiens)
Explore Q08722 
Go to UniProtKB:  Q08722
PHAROS:  Q08722
GTEx:  ENSG00000196776 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08722
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q08722-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
K [auth E],
L [auth E],
M [auth F],
N [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
H [auth D],
J [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
E, F
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.266 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.224α = 112.5
b = 79.931β = 96.61
c = 92.751γ = 103.16
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000phasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references
  • Version 1.2: 2025-08-06
    Changes: Database references