6O2V

Crystal structure of the SARAF luminal domain Cys-lock mutant monomer

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-02-24 Released: 2019-05-29 
  • Deposition Author(s): Kimberlin, C.R., Minor, D.L.
  • Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD), American Heart Association

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

SARAF Luminal Domain Structure Reveals a Novel Domain-Swapped beta-Sandwich Fold Important for SOCE Modulation.

Kimberlin, C.R.Meshcheriakova, A.Palty, R.Raveh, A.Karbat, I.Reuveny, E.Minor Jr., D.L.

(2019) J Mol Biol 431: 2869-2883

  • DOI: https://doi.org/10.1016/j.jmb.2019.05.008
  • Primary Citation of Related Structures:  
    6O2U, 6O2V, 6O2W

  • PubMed Abstract: 

    Store-Operated Calcium Entry (SOCE) plays key roles in cell proliferation, muscle contraction, immune responses, and memory formation. The coordinated interactions of a number of proteins from the plasma and endoplasmic reticulum membranes control SOCE to replenish internal Ca 2+ stores and generate intracellular Ca 2+ signals. SARAF, an endoplasmic reticulum resident component of the SOCE pathway having no homology to any characterized protein, serves as an important brake on SOCE. Here, we describe the X-ray crystal structure of the SARAF luminal domain, SARAF L . This domain forms a novel 10-stranded β-sandwich fold that includes a set of three conserved disulfide bonds, denoted the "SARAF-fold." The structure reveals a domain-swapped dimer in which the last two β-strands (β9 and β10) are exchanged forming a region denoted the "SARAF luminal switch" that is essential for dimerization. Sequence comparisons reveal that the SARAF-fold is highly conserved in vertebrates and in a variety of pathologic fungi. Förster resonance energy transfer experiments using full-length SARAF validate the formation of the domain-swapped dimer in cells and demonstrate that dimerization is reversible. A designed variant lacking the SARAF luminal switch shows that the domain swapping is essential to function and indicates that the SARAF dimer accelerates SOCE inactivation.


  • Organizational Affiliation

    Cardiovascular Research Institute, University of California, San Francisco, CA 94148, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Store-operated calcium entry-associated regulatory factor
A, B
135Homo sapiensMutation(s): 2 
Gene Names: SARAFTMEM66XTP3HSPC035NPD003PSEC0019UNQ1967/PRO4499
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BY9 (Homo sapiens)
Explore Q96BY9 
Go to UniProtKB:  Q96BY9
PHAROS:  Q96BY9
GTEx:  ENSG00000133872 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BY9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.689α = 90
b = 60.953β = 90
c = 63.441γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR01-HL080050
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)United StatesR01-DC007664
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32HL007731
American Heart AssociationUnited States14POST18740062

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description