Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.68 kDa 
• Atom Count: 777 
• Residue Count: 78 
• Unique protein chains: 1

1EDM

EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX

• DOI: 10.2210/pdb1EDM/pdb

• Classification: COAGULATION FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1996-03-21 Released: 1996-10-14 
• Deposition Author(s): Rao, Z., Handford, P., Mayhew, M., Knott, V., Brownlee, G.G., Stuart, D.

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Experimental Data Snapshot

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

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

• PubMed: 7606779 
• 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 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.

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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

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR IX	B, C	39	Homo sapiens	Mutation(s): 0  Gene Names: HUMAN FACTOR IX, F9 EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens) Explore P00740  Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740 GTEx  ENSG00000101981

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B, C	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 40.3	α = 90
b = 40.3	β = 90
c = 98.3	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
3D-SCALE	data reduction
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
3DSCALE	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-03-21 
• Released Date: 1996-10-14 
Deposition Author(s): Rao, Z., Handford, P., Mayhew, M., Knott, V., Brownlee, G.G., Stuart, D.

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