6PW7

X-ray crystal structure of C. elegans STIM EF-SAM domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Coordination of a Single Calcium Ion in the EF-hand Maintains the Off State of the Stromal Interaction Molecule Luminal Domain.

Enomoto, M.Nishikawa, T.Back, S.I.Ishiyama, N.Zheng, L.Stathopulos, P.B.Ikura, M.

(2020) J Mol Biol 432: 367-383

  • DOI: 10.1016/j.jmb.2019.10.003
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Store operated calcium (Ca 2+ ) entry (SOCE) is the process whereby endoplasmic reticulum (ER) Ca 2+ store depletion causes Orai1-composed Ca 2+ channels on the plasma membrane (PM) to open, mediating a rise in cyto ...

    Store operated calcium (Ca 2+ ) entry (SOCE) is the process whereby endoplasmic reticulum (ER) Ca 2+ store depletion causes Orai1-composed Ca 2+ channels on the plasma membrane (PM) to open, mediating a rise in cytosolic Ca 2+ levels. Stromal interaction molecules (STIMs) are the proteins that directly sense ER Ca 2+ content and gate Orai1 channels due to store depletion. The trigger for STIM activation is Ca 2+ unbinding from the ER lumen-oriented domains, which consist of a nonconserved amino (N) terminal region and EF-hand and sterile α motif (SAM) domains (EF-SAM), highly conserved from humans to Caenorhabditis elegans. Solution NMR structures of the human EF-SAM domains have been determined at high Ca 2+ concentrations; however, no direct structural view of the Ca 2+ binding mode has been elucidated. Further, no atomic resolution data currently exists on EF-SAM at low Ca 2+ levels. Here, we determined the X-ray crystal structure of the C. elegans STIM luminal domain, revealing that EF-SAM binds a single Ca 2+ ion with pentagonal bipyramidal geometry and an ancillary α-helix formed by the N-terminal region acts as a brace to stabilize EF-SAM. Using solution NMR, we observed EF-hand domain unfolding and a conformational exchange between folded and unfolded states involving the ancillary α-helix and the canonical EF-hand in low Ca 2+ . Remarkably, we also detected an α-helix (+Ca 2+ ) to β-strand (-Ca 2+ ) transition at the terminal SAM domain α-helix. Collectively, our analyses indicate that one canonically bound Ca 2+ ion is sufficient to stabilize the quiescent luminal domain structure, precluding unfolding, conformational exchange, and secondary structure transformation.


    Organizational Affiliation

    Princess Margaret Cancer Centre, Department of Medical Biophysics, University Health Network, University of Toronto, Toronto, ON M5G 1L7, Canada. Electronic address: mikura@uhnresearch.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stromal interaction molecule 1
A, B
161Caenorhabditis elegansMutation(s): 0 
Gene Names: stim-1Y55B1BM.1
Find proteins for G5EF60 (Caenorhabditis elegans)
Go to UniProtKB:  G5EF60
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.543α = 90
b = 111.58β = 90
c = 70.704γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada--

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Derived calculations
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2020-02-12
    Changes: Database references