1J34

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M300650200
  • Primary Citation of Related Structures:  1J35

  • 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 ...

    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.


    Related Citations: 
    • 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
    • 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.USA 98: 7230


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
coagulation factor IX-binding protein A chain
A
129Protobothrops flavoviridisN/A
Find proteins for Q7LZ71 (Protobothrops flavoviridis)
Go to UniProtKB:  Q7LZ71
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
coagulation factor IX-binding protein B chain
B
123Protobothrops flavoviridisN/A
Find proteins for P23807 (Protobothrops flavoviridis)
Go to UniProtKB:  P23807
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
C
46Bos taurusGene Names: F9
EC: 3.4.21.22
Find proteins for P00741 (Bos taurus)
Go to Gene View: F9
Go to UniProtKB:  P00741
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
C
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.552α = 90.00
b = 37.204β = 103.56
c = 62.626γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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