8IVD | pdb_00008ivd

COMPLEX STRUCTURE OF CD93-IGFBP7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 
    0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insight into CD93 recognition by IGFBP7.

Xu, Y.Sun, Y.Zhu, Y.Song, G.

(2024) Structure 32: 282-291.e4

  • DOI: https://doi.org/10.1016/j.str.2023.12.011
  • Primary Citation of Related Structures:  
    8IVD

  • PubMed Abstract: 

    The CD93/IGFBP7 axis proteins are key factors expressed in endothelial cells (EC) that mediate EC angiogenesis and migration. Their upregulation contributes to tumor vascular abnormality and a blockade of this interaction promotes a favorable tumor microenvironment for therapeutic interventions. However, the interactions of these proteins with each other remain unclear. In this study, we determined a partial structure of the human CD93-IGFBP7 complex comprising the EGF 1 domain of CD93 and the IB domain of IGFBP7. Mutagenesis studies confirmed interactions and specificities. Cellular and mouse tumor studies demonstrated the physiological relevance of the CD93-IGFBP7 interaction in EC angiogenesis. Our study provides leads for the development of therapeutic agents to precisely disrupt unwanted CD93-IGFBP7 signaling in the tumor microenvironment. Additionally, analysis of the CD93 full-length architecture provides insights into how CD93 protrudes on the cell surface and forms a flexible platform for binding to IGFBP7 and other ligands.


  • Organizational Affiliation
    • Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor-binding protein 7,Complement component C1q receptor
A, B, C, D
481Homo sapiensMutation(s): 0 
Gene Names: IGFBP7MAC25PSFCD93C1QR1MXRA4
UniProt & NIH Common Fund Data Resources
Find proteins for Q16270 (Homo sapiens)
Explore Q16270 
Go to UniProtKB:  Q16270
PHAROS:  Q16270
GTEx:  ENSG00000163453 
Find proteins for Q9NPY3 (Homo sapiens)
Explore Q9NPY3 
Go to UniProtKB:  Q9NPY3
PHAROS:  Q9NPY3
GTEx:  ENSG00000125810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ16270Q9NPY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free:  0.302 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.512α = 90
b = 208.895β = 90
c = 77.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171215

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Structure summary