1MA9 | pdb_00001ma9

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), 0.246 (DCC)
R-Value Work:
0.200 (Depositor), 0.197 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 12554937 Search on PubMed
DOI: https://doi.org/10.1107/s0907444902021455
Primary Citation 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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02774
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on 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), 0.246 (DCC)
R-Value Work: 0.200 (Depositor), 0.197 (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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-02-04

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary