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- PDB-6pw7: X-ray crystal structure of C. elegans STIM EF-SAM domain -

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Basic information

Entry
Database: PDB / ID: 6pw7
TitleX-ray crystal structure of C. elegans STIM EF-SAM domain
ComponentsStromal interaction molecule 1
KeywordsSIGNALING PROTEIN / Stromal interaction molecule (STIM) / EF-hand / SAM-domain / Calcium release-activated channels / Store operated calcium entry (SOCE)
Function / homology
Function and homology information


Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ion homeostasis / positive regulation of engulfment of apoptotic cell / ovulation / store-operated calcium entry / : / intracellular organelle / positive regulation of smooth muscle contraction / calcium channel regulator activity / calcium channel activity ...Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ion homeostasis / positive regulation of engulfment of apoptotic cell / ovulation / store-operated calcium entry / : / intracellular organelle / positive regulation of smooth muscle contraction / calcium channel regulator activity / calcium channel activity / intracellular calcium ion homeostasis / neuronal cell body / calcium ion binding / dendrite / endoplasmic reticulum / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Recoverin; domain 1 - #180 / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Recoverin; domain 1 / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 ...Recoverin; domain 1 - #180 / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Recoverin; domain 1 / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Stromal interaction molecule 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsEnomoto, M. / Nishikawa, T. / Back, S.I. / Ishiyama, N. / Zheng, L. / Stathopulos, P.B. / Ikura, M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Coordination of a Single Calcium Ion in the EF-hand Maintains the Off State of the Stromal Interaction Molecule Luminal Domain.
Authors: Enomoto, M. / Nishikawa, T. / Back, S.I. / Ishiyama, N. / Zheng, L. / Stathopulos, P.B. / Ikura, M.
History
DepositionJul 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stromal interaction molecule 1
B: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1554
Polymers38,0752
Non-polymers802
Water6,089338
1
A: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0782
Polymers19,0381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0782
Polymers19,0381
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.543, 111.580, 70.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11B-466-

HOH

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Components

#1: Protein Stromal interaction molecule 1


Mass: 19037.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: stim-1, Y55B1BM.1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EF60
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.42 % / Description: needle
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 18% v/v PEG 3,350, 8% v/v tacsimate, 10mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97873, 0.97903, 0.9746, 0.98321
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978731
20.979031
30.97461
40.983211
ReflectionResolution: 1.82→50 Å / Num. obs: 39514 / % possible obs: 98.7 % / Redundancy: 14.5 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 1867 / CC1/2: 0.183

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 1.89→43.8 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2355 1666 4.99 %
Rwork0.1873 --
obs0.1897 33407 93.62 %
Refinement stepCycle: LAST / Resolution: 1.89→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 2 338 2988
LS refinement shellResolution: 1.89→1.9456 Å
RfactorNum. reflection% reflection
Rfree0.3658 --
Rwork0.3605 --
obs-2810 84 %

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