Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.14 kDa 
• Atom Count: 2364 
• Modelled Residue Count: 305 
• Deposited Residue Count: 323 
• Unique protein chains: 1

1IJ5

METAL-FREE STRUCTURE OF MULTIDOMAIN EF-HAND PROTEIN, CBP40, FROM TRUE SLIME MOLD

• PDB DOI: 10.2210/pdb1IJ5/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Physarum polycephalum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-04-25 Released: 2003-02-11 
• Deposition Author(s): Iwasaki, W., Sasaki, H., Nakamura, A., Kohama, K., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.244 

Literature

Metal-Free and Ca(2+)-Bound Structures of a Multidomain EF-Hand Protein, CBP40, from the Lower Eukaryote Physarum polycephalum

Iwasaki, W., Sasaki, H., Nakamura, A., Kohama, K., Tanokura, M.

(2003) Structure 11: 75-85

• PubMed: 12517342 
• DOI: 10.1016/s0969-2126(02)00932-2
• Primary Citation of Related Structures:  
  1IJ5, 1IJ6


• PubMed Abstract: 
  

Acellular slime mold, Physarum polycephalum, has a unique wound-healing system. When cytoplasm of plasmodia is exposed to extracellular fluid, calcium binding protein 40 (CBP40) seals damaged areas, forming large aggregates Ca(2+) dependently. Part of the CBP40 is truncated at the N terminus by a proteinase in plasmodia (CBP40delta), which does not aggregate in the Ca(2+)-bound form. Here we report the crystal structures of CBP40delta in both the metal-free and the Ca(2+)-bound states. Both structures consist of three domains: coiled-coil, intervening, and EF-hand. The topology of the EF-hand domain is similar to that of calpain. The N-terminal half of CBP40Delta interacts with the C-terminal EF-hands through a large hydrophobic interface, necessary for high Ca(2+) affinity. Conformational change upon Ca(2+) binding is small; however, the structure of CBP40delta provides novel insights into the mechanism of Ca(2+)-dependent oligomerization.

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Organizational Affiliation: 

Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PLASMODIAL SPECIFIC LAV1-2 PROTEIN	A	323	Physarum polycephalum	Mutation(s): 0
UniProt
Find proteins for P14725 (Physarum polycephalum) Explore P14725  Go to UniProtKB:  P14725

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.260 
• R-Value Work: 0.244 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.4	α = 90
b = 64.4	β = 90
c = 207.2	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
MLPHARE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-25 
• Released Date: 2003-02-11 
Deposition Author(s): Iwasaki, W., Sasaki, H., Nakamura, A., Kohama, K., Tanokura, M.

Revision History  

• Version 1.0: 2003-02-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance