2BE4

X-RAY STRUCTURE AN EF-HAND PROTEIN FROM DANIO RERIO Dr.36843


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

X-ray structure of Danio rerio secretagogin: A hexa-EF-hand calcium sensor.

Bitto, E.Bingman, C.A.Bittova, L.Frederick, R.O.Fox, B.G.Phillips Jr., G.N.

(2009) Proteins 76: 477-483

  • DOI: 10.1002/prot.22362
  • Primary Citation of Related Structures:  
    2BE4

  • PubMed Abstract: 
  • Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hex ...

    Many essential physiological processes are regulated by the modulation of calcium concentration in the cell. The EF-hand proteins represent a superfamily of calcium-binding proteins involved in calcium signaling and homeostasis. Secretagogin is a hexa-EF-hand protein that is highly expressed in pancreatic islet of Langerhans and neuroendocrine cells and may play a role in the trafficking of secretory granules. We present the X-ray structure of Danio rerio secretagogin, which is 73% identical to human secretagogin, in calcium-free form at 2.1-A resolution. Secretagogin consists of the three globular domains each of which contains a pair of EF-hand motifs. The domains are arranged into a V-shaped molecule with a distinct groove formed at the interface of the domains. Comparison of the secretagogin structure with the solution structure of calcium-loaded calbindin D(28K) revealed a striking difference in the spatial arrangement of their domains, which involves approximately 180 degrees rotation of the first globular domain with respect to the module formed by the remaining domains.


    Organizational Affiliation

    Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706-1544, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical protein LOC449832A272Danio rerioMutation(s): 10 
Gene Names: Dr.36843BC083168scgnzgc:100843
Find proteins for Q5XJX1 (Danio rerio)
Explore Q5XJX1 
Go to UniProtKB:  Q5XJX1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.884α = 90
b = 52.748β = 90
c = 114.364γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
SHELXDphasing
SOLOMONphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2013-02-06
    Changes: Database references
  • Version 1.4: 2017-10-18
    Changes: Refinement description