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- PDB-6aki: Calcium release-activated calcium channel protein 1, P288L mutant -

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Basic information

Entry
Database: PDB / ID: 6aki
TitleCalcium release-activated calcium channel protein 1, P288L mutant
ComponentsCalcium release-activated calcium channel protein 1
KeywordsMEMBRANE PROTEIN / Calcium Channel
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 superfamily / Mediator of CRAC channel activity
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 / Resolution: 4.496 Å
AuthorsLiu, X. / Wu, G. / Yang, X. / Shen, Y.
CitationJournal: To Be Published
Title: Calcium release-activated calcium channel protein 1, P288L mutant
Authors: Liu, X. / Wu, G. / Yang, X. / Shen, Y.
History
DepositionSep 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
C: Calcium release-activated calcium channel protein 1
D: Calcium release-activated calcium channel protein 1
E: Calcium release-activated calcium channel protein 1
F: Calcium release-activated calcium channel protein 1
O: Calcium release-activated calcium channel protein 1
P: Calcium release-activated calcium channel protein 1
Q: Calcium release-activated calcium channel protein 1
R: Calcium release-activated calcium channel protein 1
S: Calcium release-activated calcium channel protein 1
T: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,00716
Polymers284,86612
Non-polymers1424
Water00
1
A: Calcium release-activated calcium channel protein 1
B: Calcium release-activated calcium channel protein 1
C: Calcium release-activated calcium channel protein 1
D: Calcium release-activated calcium channel protein 1
E: Calcium release-activated calcium channel protein 1
F: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5048
Polymers142,4336
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19210 Å2
ΔGint-270 kcal/mol
Surface area44600 Å2
MethodPISA
2
O: Calcium release-activated calcium channel protein 1
P: Calcium release-activated calcium channel protein 1
Q: Calcium release-activated calcium channel protein 1
R: Calcium release-activated calcium channel protein 1
S: Calcium release-activated calcium channel protein 1
T: Calcium release-activated calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5048
Polymers142,4336
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19610 Å2
ΔGint-274 kcal/mol
Surface area44910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.107, 90.659, 178.721
Angle α, β, γ (deg.)90.00, 106.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23738.793 Da / Num. of mol.: 12 / Fragment: UNP residues 132-341 / Mutation: P288L, C283T, C224S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Cell line (production host): HEK293S-GnTi- / Production host: Homo sapiens (human) / References: UniProt: Q9U6B8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl

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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: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.05M NaCl,0.02M MgCl2, 0.1M Sodium citrate pH 6.5, 16-20% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.49→50 Å / Num. obs: 17659 / % possible obs: 80.7 % / Redundancy: 3.5 % / Net I/σ(I): 7.94
Reflection shellResolution: 4.49→4.66 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.496→26.475 Å / SU ML: 1.02 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 47.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3862 2958 10.09 %
Rwork0.3246 --
obs0.3306 17659 69.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.496→26.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12372 0 4 0 12376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412540
X-RAY DIFFRACTIONf_angle_d0.92817124
X-RAY DIFFRACTIONf_dihedral_angle_d2.9247356
X-RAY DIFFRACTIONf_chiral_restr0.0472340
X-RAY DIFFRACTIONf_plane_restr0.0062016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.4964-4.56970.389410.3374362X-RAY DIFFRACTION20
4.5697-4.64810.355460.3332369X-RAY DIFFRACTION21
4.6481-4.73220.3553550.3352431X-RAY DIFFRACTION24
4.7322-4.82260.4007610.3073457X-RAY DIFFRACTION26
4.8226-4.92050.4504570.2953598X-RAY DIFFRACTION32
4.9205-5.02670.4146820.2639716X-RAY DIFFRACTION40
5.0267-5.14290.4643970.2931873X-RAY DIFFRACTION48
5.1429-5.27050.5321190.32961054X-RAY DIFFRACTION59
5.2705-5.41180.45761440.3671318X-RAY DIFFRACTION74
5.4118-5.56960.44111800.40981607X-RAY DIFFRACTION90
5.5696-5.74760.45211770.41021687X-RAY DIFFRACTION92
5.7476-5.95080.41931890.43061692X-RAY DIFFRACTION94
5.9508-6.18620.43811960.42231661X-RAY DIFFRACTION93
6.1862-6.46380.38981800.39881712X-RAY DIFFRACTION94
6.4638-6.79920.47741920.40441630X-RAY DIFFRACTION92
6.7992-7.2170.45941740.38621656X-RAY DIFFRACTION92
7.217-7.76120.41821900.34371777X-RAY DIFFRACTION97
7.7612-8.51860.32721980.26551722X-RAY DIFFRACTION98
8.5186-9.69780.2882070.23861759X-RAY DIFFRACTION97
9.6978-12.02460.30411830.25781664X-RAY DIFFRACTION92
12.0246-26.47510.38681900.35161609X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 105.4684 Å / Origin y: -80.5324 Å / Origin z: 43.3799 Å
111213212223313233
T0.7409 Å20.21 Å2-0.4297 Å2-1.4671 Å2-0.0568 Å2--0.8579 Å2
L2.3964 °20.8889 °22.2316 °2-0.3474 °20.7191 °2--2.3416 °2
S0.0194 Å °0.3643 Å °0.0405 Å °-0.1877 Å °0.089 Å °0.1461 Å °0.0886 Å °0.1999 Å °0.038 Å °
Refinement TLS groupSelection details: all

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