1MA9

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

• PDB DOI: https://doi.org/10.2210/pdb1MA9/pdb

• Classification: TRANSPORT PROTEIN/CONTRACTILE PROTEIN
• Organism(s): Homo sapiens, Oryctolagus cuniculus
• Mutation(s): Yes 


• Deposited: 2002-08-02 Released: 2003-02-04 
• Deposition Author(s): Verboven, C., Bogaerts, I., Waelkens, E., Rabijns, A., Van Baelen, H., Bouillon, R., De Ranter, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

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

• PubMed: 12554937 
• DOI: https://doi.org/10.1107/s0907444902021455
• Primary Citation of Related Structures:  
  1MA9


• 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 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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 93.7 kDa 
• Atom Count: 6,441 
• Modelled Residue Count: 799 
• Deposited Residue Count: 833 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D-binding protein	A	458	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02774 (Homo sapiens) Explore P02774  Go to UniProtKB:  P02774
PHAROS:  P02774 GTEx:  ENSG00000145321

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, Alpha Skeletal Muscle	B	375	Oryctolagus cuniculus	Mutation(s): 1  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	B	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.44	α = 90
b = 74.9	β = 110.19
c = 88.02	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Verboven, C., Bogaerts, I., Waelkens, E., Rabijns, A., Van Baelen, H., Bouillon, R., De Ranter, C.

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