1MA9

Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Actin-DBP: the perfect structural fit?

Verboven, C.Bogaerts, I.Waelkens, E.Rabijns, A.Van Baelen, H.Bouillon, R.De Ranter, C.

(2003) Acta Crystallogr D Biol Crystallogr 59: 263-273

  • DOI: 10.1107/s0907444902021455
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The multifunctional vitamin D binding protein (DBP) is an actin-sequestering protein present in blood. The crystal structure of the actin-DBP complex was determined at 2.4 A resolution. DBP binds to actin subdomains 1 and 3 and occludes the cleft at ...

    The multifunctional vitamin D binding protein (DBP) is an actin-sequestering protein present in blood. The crystal structure of the actin-DBP complex was determined at 2.4 A resolution. DBP binds to actin subdomains 1 and 3 and occludes the cleft at the interface between these subdomains. Most remarkably, DBP demonstrates an unusually large actin-binding interface, far exceeding the binding-interface areas reported for other actin-binding proteins such as profilin, DNase I and gelsolin. The fast-growing side of actin monomers is blocked completely through a perfect structural fit with DBP, demonstrating how DBP effectively interferes with actin-filament formation. It establishes DBP as the hitherto best actin-sequestering protein and highlights its key role in suppressing and preventing extracellular actin polymerization.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray investigation of the complex of the human vitamin D binding protein and rabbit muscle actin
      Bogaerts, I., Verboven, C., Rabijns, A., Waelkens, E., Van Baelen, H., De Ranter, C.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 740
    • A structural basis for the unique binding features of the human vitamin D-binding protein
      Verboven, C., Rabijns, A., De Maeyer, M., Van Baelen, H., Bouillon, R., De Ranter, C.
      (2002) Nat Struct Biol 9: 131
    • Atomic structure of the actin:DNase I complex
      Kabsch, W., Mannherz, H.G., Suck, D., Pai, E.F., Holmes, K.C.
      (1990) Nature 347: 37

    Organizational Affiliation

    Laboratorium voor Analytische Chemie en Medicinale Fysicochemie, Faculteit Farmaceutische Wetenschappen, K. U. Leuven, Belgium.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D-binding protein
A
458Homo sapiensMutation(s): 0 
Gene Names: GC
Find proteins for P02774 (Homo sapiens)
Go to UniProtKB:  P02774
NIH Common Fund Data Resources
PHAROS  P02774

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin, Alpha Skeletal Muscle
B
375Oryctolagus cuniculusMutation(s): 1 
Gene Names: ACTA1ACTA
Find proteins for P68135 (Oryctolagus cuniculus)
Go to UniProtKB:  P68135
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
B
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
B
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.44α = 90
b = 74.9β = 110.19
c = 88.02γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance