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- PDB-4hkr: Calcium release-activated calcium (CRAC) channel ORAI -

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Basic information

Entry
Database: PDB / ID: 4hkr
TitleCalcium release-activated calcium (CRAC) channel ORAI
ComponentsCalcium release-activated calcium channel protein 1
KeywordsTRANSPORT PROTEIN / calcium channel / Orai1 / eukaryotic membrane protein / membrane protein / ion channel / STIM / membrane
Function / homology
Function and homology information


store-operated calcium entry / store-operated calcium channel activity / positive regulation of calcineurin-NFAT signaling cascade / positive regulation of calcium ion transport / calcium channel regulator activity / calcium channel complex / calcium ion transmembrane transport / calcium channel activity / identical protein binding / membrane / plasma membrane
Similarity search - Function
Calcium release-activated calcium channel protein Orai / Calcium release-activated calcium channel protein / Orai superfamily / Mediator of CRAC channel activity / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / Calcium release-activated calcium channel protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / Resolution: 3.3511 Å
AuthorsLong, S.B. / Hou, X.
CitationJournal: Science / Year: 2012
Title: Crystal structure of the calcium release-activated calcium channel Orai.
Authors: Hou, X. / Pedi, L. / Diver, M.M. / Long, S.B.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0096
Polymers48,6952
Non-polymers3144
Water00
1
A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
hetero molecules

A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
hetero molecules

A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,02818
Polymers146,0846
Non-polymers94312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area23840 Å2
ΔGint-335 kcal/mol
Surface area39820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.910, 117.910, 117.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-401-

BA

21A-402-

ZN

31A-403-

FE

41A-404-

FE

DetailsThe biological assembly is a hexamer generated from the dimer in the asymmetric unit by the three fold crystallographic axis

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Components

#1: Protein Calcium release-activated calcium channel protein 1 / Protein orai / dOrai


Mass: 24347.395 Da / Num. of mol.: 2 / Fragment: UNP Residues 133-341 / Mutation: C224S, C283T, P276R, P277R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: olf186-F, CRACM1, olf186, CG11430 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9U6B8
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 400, 1 M Ammonium Formate, 100 mM MES pH 6.5. The crystal was soaked in: 50 % PEG 400, 1 M Ammonium Formate, 100 mM MES pH 6.5, 50 mM barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.35→40 Å / Num. all: 8116 / Num. obs: 8116 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 40.5 % / Biso Wilson estimate: 152 Å2 / Rsym value: 0.072 / Net I/σ(I): 59.7
Reflection shellResolution: 3.35→3.41 Å / Redundancy: 40.7 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 386 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
PHASERphasing
PHENIX(1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
CNS(1.3)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: PDB ENTRY 4HKS

4hks


Resolution: 3.3511→19.93 Å / SU ML: 0.31 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 39.72 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2794 401 5.02 %Random
Rwork0.278 ---
all0.278 8057 --
obs0.278 7995 99.23 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 170 Å2
Refinement stepCycle: LAST / Resolution: 3.3511→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 4 0 2350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092399
X-RAY DIFFRACTIONf_angle_d1.3363268
X-RAY DIFFRACTIONf_dihedral_angle_d15.346762
X-RAY DIFFRACTIONf_chiral_restr0.082411
X-RAY DIFFRACTIONf_plane_restr0.005387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3511-3.8330.33371100.30852527X-RAY DIFFRACTION100
3.833-4.81790.33321450.30492470X-RAY DIFFRACTION98
4.8179-19.93080.2551460.26332597X-RAY DIFFRACTION100

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