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- PDB-3teq: Crystal structure of SOAR domain -

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Basic information

Entry
Database: PDB / ID: 3teq
TitleCrystal structure of SOAR domain
ComponentsStromal interaction molecule 1STIM1
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / cortical endoplasmic reticulum / enamel mineralization / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / calcium channel regulator activity ...store-operated calcium entry / activation of store-operated calcium channel activity / regulation of store-operated calcium entry / cortical endoplasmic reticulum / enamel mineralization / Elevation of cytosolic Ca2+ levels / positive regulation of adenylate cyclase activity / microtubule plus-end binding / plasma membrane raft / calcium channel regulator activity / regulation of calcium ion transport / detection of calcium ion / Ion homeostasis / sarcoplasmic reticulum membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / intracellular calcium ion homeostasis / positive regulation of angiogenesis / protease binding / microtubule / calcium ion binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / plasma membrane
Similarity search - Function
Helix Hairpins - #3550 / Stromal interaction molecule 1, SAM domain / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Helix Hairpins - #3550 / Stromal interaction molecule 1, SAM domain / Stromal interaction molecule, Orai1-activating region / Stromal interaction molecule / STIM1 Orai1-activating region / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Stromal interaction molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsYang, X. / Jin, H. / Cai, X. / Shen, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into the activation of Stromal interaction molecule 1 (STIM1).
Authors: Yang, X. / Jin, H. / Cai, X. / Li, S. / Shen, Y.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,3289
Polymers46,8544
Non-polymers4755
Water10,503583
1
A: Stromal interaction molecule 1
C: Stromal interaction molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9027
Polymers23,4272
Non-polymers4755
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-47 kcal/mol
Surface area13870 Å2
MethodPISA
2
B: Stromal interaction molecule 1

B: Stromal interaction molecule 1


Theoretical massNumber of molelcules
Total (without water)23,4272
Polymers23,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area1670 Å2
ΔGint-18 kcal/mol
Surface area13730 Å2
MethodPISA
3
D: Stromal interaction molecule 1

D: Stromal interaction molecule 1


Theoretical massNumber of molelcules
Total (without water)23,4272
Polymers23,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_664-y+1,-x+1,-z-1/21
Buried area1740 Å2
ΔGint-18 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.584, 90.584, 104.919
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Stromal interaction molecule 1 / STIM1


Mass: 11713.393 Da / Num. of mol.: 4 / Fragment: SOAR domain (UNP RESIDUES 344-444) / Mutation: L374M, V419A, C437T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STIM1, GOK / Production host: Escherichia coli (E. coli) / References: UniProt: Q13586
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 10% PEG3350, 0.2M Ammonium dibasic phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9792
SYNCHROTRONSSRF BL17U20.9792
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMar 22, 2010
MARMOSAIC 225 mm CCD2CCDMay 22, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 40114 / Num. obs: 36416 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.079 / Net I/σ(I): 2.9
Reflection shellResolution: 1.8→1.86 Å / % possible all: 66.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→25.2 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2320392.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1749 5 %RANDOM
Rwork0.219 ---
all0.221 36638 --
obs0.219 34889 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9755 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.91 Å20 Å20 Å2
2---4.91 Å20 Å2
3---9.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 25 583 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.862
X-RAY DIFFRACTIONc_scbond_it2.522
X-RAY DIFFRACTIONc_scangle_it3.772.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 279 5 %
Rwork0.258 5356 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3po4.parampo4.top

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