8IVD

COMPLEX STRUCTURE OF CD93-IGFBP7

• PDB DOI: https://doi.org/10.2210/pdb8IVD/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-03-27 Released: 2024-01-17 
• Deposition Author(s): Xu, Y.M., Song, G.J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.302 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Literature

structural insight into CD93 recognition by IGFBP7

Xu, Y.M., Song, G.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 201.32 kDa 
• Atom Count: 5,380 
• Modelled Residue Count: 764 
• Deposited Residue Count: 1,924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin-like growth factor-binding protein 7,Complement component C1q receptor	A, B, C, D	481	Homo sapiens	Mutation(s): 0  Gene Names: IGFBP7, MAC25, PSF, CD93, C1QR1, MXRA4
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
UniProt Groups	Q16270Q9NPY3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.302 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.512	α = 90
b = 208.895	β = 90
c = 77.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Xu, Y.M., Song, G.J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171215

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release