Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 35.69 kDa 
• Atom Count: 2756 
• Residue Count: 298 
• Unique protein chains: 3

1J35

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

• DOI: 10.2210/pdb1J35/pdb

• Classification: Protein binding/Blood clotting
• Organism(s): Protobothrops flavoviridis, Bos taurus
• Mutation(s): Yes 


• Deposited: 2003-01-20 Released: 2003-07-08 
• Deposition Author(s): Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 

Literature

Crystal Structure of Mg2+- and Ca2+-bound Gla Domain of Factor IX Complexed with Binding Protein

Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

(2003) J Biol Chem 278: 24090-24094

• PubMed: 12695512 
• DOI: 10.1074/jbc.M300650200
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Factor IX is an indispensable protein required in the blood coagulation cascade. It binds to the surface of phospholipid membrane by means of a gamma-carboxyglutamic acid (Gla) domain situated at the N terminus. Recently, we showed that physiological concentrations of Mg2+ ions affect the native conformation of the Gla domain and in doing so augment the biological activity of factor IXa and binding affinity with its binding protein even in the presence of Ca2+ ions. Here we report on the crystal structures of the Mg2+/Ca2+-bound and Ca2+-bound (Mg2+-free) factor IX Gla domain (IXGD1-46) in complex with its binding protein (IX-bp) at 1.55 and 1.80 A resolutions, respectively. Three Mg2+ and five Ca2+ ions were bound in the Mg2+/Ca2+-bound IXGD1-46, and the Mg2+ ions were replaced by Ca2+ ions in Mg2+-free IXGD1-46. Comparison of Mg2+/Ca2+-bound with Ca2+-bound structures of the complexes showed that Mg2+ ion, which formed a bridge between IXGD1-46 and IX-bp, forced IXGD1-46 to rotate 4 degrees relative to IX-bp and hence might be the cause of a more tight interaction between the molecules than in the case of the Mg2+-free structure. The results clearly suggest that Mg2+ ions are required to maintain native conformation and in vivo function of factor IX Gla domain during blood coagulation.

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Related Citations: 

• Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X
  Mizuno, H., Fujimoto, Z., Atoda, H., Morita, T.
  (2001) Proc Natl Acad Sci U S A 98: 7230

• Crystal structure of coagulation factor IX-binding protein from habu snake venom at 2.6 A: implication of central loop swapping based on deletion in the linker region
  Mizuno, H., Fujimoto, Z., Koizumi, M., Kano, H., Atoda, H., Morita, T.
  (1999) J Mol Biol 289: 103

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Organizational Affiliation: 

Department of Biochemistry, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
coagulation factor IX-binding protein A chain	A	129	Protobothrops flavoviridis	Mutation(s): 0
Find proteins for P23806 (Protobothrops flavoviridis) Go to UniProtKB:  P23806

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor IX-binding protein B chain	B	123	Protobothrops flavoviridis	Mutation(s): 0
Find proteins for P23807 (Protobothrops flavoviridis) Go to UniProtKB:  P23807

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor IX	C	46	Bos taurus	Mutation(s): 12  Gene Names: F9 EC: 3.4.21.22
Find proteins for P00741 (Bos taurus) Go to UniProtKB:  P00741

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	C	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.270 
• R-Value Work: 0.227 
• R-Value Observed: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.959	α = 90
b = 39.074	β = 99.56
c = 63.949	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-01-20 
• Released Date: 2003-07-08 
Deposition Author(s): Shikamoto, Y., Morita, T., Fujimoto, Z., Mizuno, H.

Revision History 

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance