1GJY | pdb_00001gjy

The X-ray structure of the Sorcin Calcium Binding Domain (SCBD) provides insight into the phosphorylation and calcium dependent processess


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.296 (Depositor) 
  • R-Value Work: 
    0.232 (Depositor) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1GJY

This is version 1.3 of the entry. See complete history

Literature

The Crystal Structure of the Sorcin Calcium Binding Domain Provides a Model of Ca(2+)-Dependent Processes in the Full-Length Protein

Ilari, A.Johnson, K.Nastopoulos, V.Verzili, D.Zamparelli, C.Colotti, G.Tsernoglou, D.Chiancone, E.

(2002) J Mol Biology 317: 447

  • DOI: https://doi.org/10.1006/jmbi.2002.5417
  • Primary Citation Related Structures: 
    1GJY

  • PubMed Abstract: 

    Sorcin is a 21.6 kDa calcium binding protein, expressed in a number of mammalian tissues that belongs to the small, recently identified penta-EF-hand (PEF) family. Like all members of this family, sorcin undergoes a Ca2+-dependent translocation from cytosol to membranes where it binds to target proteins. For sorcin, the targets differ in different tissues, indicating that it takes part in a number of Ca2+-regulated processes. The sorcin monomer is organized in two domains like in all PEF proteins: a flexible, hydrophobic, glycine-rich N-terminal region and a calcium binding C-terminal domain. In vitro, the PEF proteins are dimeric in their Ca2+-free form, but have a marked tendency to precipitate when bound to calcium. Stabilization of the dimeric structure is achieved by pairing of the uneven EF-hand, EF5. Sorcin can also form tetramers at acid pH. The sorcin calcium binding domain (SCBD, residues 33-198) expressed in Escherichia coli was crystallized in the Ca2+-free form. The structure was solved by molecular replacement and was refined to 2.2 A with a crystallographic R-factor of 22.4 %. Interestingly, the asymmetric unit contains two dimers. The structure of the SCBD leads to a model that explains the solution properties and describes the Ca2+-induced conformational changes. Phosphorylation studies show that the N-terminal domain hinders phosphorylation of SCBD, i.e. the rate of phosphorylation increased twofold in the absence of the N-terminal region. In addition, previous fluorescence studies indicated that hydrophobic residues are exposed to solvent upon Ca2+ binding to full-length sorcin. The model accounts for these data by proposing that Ca2+ binding weakens the interactions between the two domains and leads to their reorientation, which exposes hydrophobic regions facilitating the Ca2+-dependent binding to target proteins at or near membranes.


  • Organizational Affiliation
    • CNR, Centro Studio sulla Biologia Molecolare and Dipartimento di Scienze Biochimiche, Università La Sapienza, P.le Aldo Moro 5, Roma, 00185, Italy.

Macromolecule Content 

  • Total Structure Weight: 76.09 kDa 
  • Atom Count: 5,615 
  • Modeled Residue Count: 668 
  • Deposited Residue Count: 668 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SORCIN
A, B, C, D
167Cricetulus griseusMutation(s): 0 
UniProt
Find proteins for P05044 (Cricetulus griseus)
Explore P05044 
Go to UniProtKB:  P05044
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05044
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.296 (Depositor) 
  • R-Value Work:  0.232 (Depositor) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.925α = 90
b = 103.847β = 117.96
c = 78.546γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-04-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations