1EDM

EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein-protein interactions.

Rao, Z.Handford, P.Mayhew, M.Knott, V.Brownlee, G.G.Stuart, D.

(1995) Cell 82: 131-141

  • DOI: 10.1016/0092-8674(95)90059-4
  • Primary Citation of Related Structures:  
    1EDM

  • PubMed Abstract: 
  • Various diverse extracellular proteins possess Ca(2+)-binding epidermal growth factor (EGF)-like domains, the function of which remains uncertain. We have determined, at high resolution (1.5 A), the crystal structure of such a domain, from human clot ...

    Various diverse extracellular proteins possess Ca(2+)-binding epidermal growth factor (EGF)-like domains, the function of which remains uncertain. We have determined, at high resolution (1.5 A), the crystal structure of such a domain, from human clotting factor IX, as a complex with Ca2+. The Ca2+ ligands form a classic pentagonal bipyramid with six ligands contributed by one polypeptide chain and the seventh supplied by a neighboring EGF-like domain. The crystal structure identifies the role of Ca2+ in maintaining the conformation of the N-terminal region of the domain, but more importantly demonstrates that Ca2+ can directly mediate protein-protein contacts. The observed crystal packing of the domains provides a plausible model for the association of multiple tandemly linked EGF-like domains in proteins such as fibrillin-1, Notch, and protein S. This model is consistent with the known functional data and suggests a general biological role for these domains.


    Related Citations: 
    • Crystallization of a Calcium-Binding Egf-Like Domain
      Rao, Z., Handford, P., Mayhew, M., Knott, V., Brownlee, G.G., Stuart, D.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 402

    Organizational Affiliation

    Laboratory of Molecular Biophysics, University of Oxford, England.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR IXBC39Homo sapiensMutation(s): 0 
Gene Names: HUMAN FACTOR IXF9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.157 
  • R-Value Observed: 0.157 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.3α = 90
b = 40.3β = 90
c = 98.3γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
3D-SCALEdata reduction
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
3DSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-10-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance