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- PDB-6bbh: The CRAC channel Orai in an unlatched-closed conformation; K163W ... -

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Basic information

Entry
Database: PDB / ID: 6bbh
TitleThe CRAC channel Orai in an unlatched-closed conformation; K163W loss-of-function mutation
ComponentsCalcium release-activated calcium channel protein 1
KeywordsMEMBRANE PROTEIN / ion channel / calcium / SOCE / CRAC / eukaryotic / open structure
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 / nervous system development / membrane ...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 / nervous system development / membrane / identical protein binding / 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 / MIRAS / Resolution: 6.1 Å
AuthorsLong, S.B. / Hou, X. / Burstein, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM094273 United States
CitationJournal: Elife / Year: 2018
Title: Structures reveal opening of the store-operated calcium channel Orai.
Authors: Hou, X. / Burstein, S.R. / Long, S.B.
History
DepositionOct 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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
G: Calcium release-activated calcium channel protein 1
H: Calcium release-activated calcium channel protein 1
I: Calcium release-activated calcium channel protein 1
J: Calcium release-activated calcium channel protein 1
K: Calcium release-activated calcium channel protein 1
L: Calcium release-activated calcium channel protein 1
M: Calcium release-activated calcium channel protein 1
N: 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
U: Calcium release-activated calcium channel protein 1
V: Calcium release-activated calcium channel protein 1
W: Calcium release-activated calcium channel protein 1
X: Calcium release-activated calcium channel protein 1


Theoretical massNumber of molelcules
Total (without water)582,82224
Polymers582,82224
Non-polymers00
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


Theoretical massNumber of molelcules
Total (without water)145,7066
Polymers145,7066
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21640 Å2
ΔGint-297 kcal/mol
Surface area44990 Å2
MethodPISA
2
G: Calcium release-activated calcium channel protein 1
H: Calcium release-activated calcium channel protein 1
I: Calcium release-activated calcium channel protein 1
J: Calcium release-activated calcium channel protein 1
K: Calcium release-activated calcium channel protein 1
L: Calcium release-activated calcium channel protein 1


Theoretical massNumber of molelcules
Total (without water)145,7066
Polymers145,7066
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-297 kcal/mol
Surface area44790 Å2
MethodPISA
3
M: Calcium release-activated calcium channel protein 1
N: 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


Theoretical massNumber of molelcules
Total (without water)145,7066
Polymers145,7066
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-300 kcal/mol
Surface area44600 Å2
MethodPISA
4
S: Calcium release-activated calcium channel protein 1
T: Calcium release-activated calcium channel protein 1
U: Calcium release-activated calcium channel protein 1
V: Calcium release-activated calcium channel protein 1
W: Calcium release-activated calcium channel protein 1
X: Calcium release-activated calcium channel protein 1


Theoretical massNumber of molelcules
Total (without water)145,7066
Polymers145,7066
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22040 Å2
ΔGint-300 kcal/mol
Surface area44580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)247.459, 247.459, 210.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

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


Mass: 24284.268 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: olf186-F, CRACM1, olf186, CG11430 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9U6B8

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28% PEG 400 150 mM NaCl 100 mM HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 6.1→50 Å / Num. obs: 15295 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 22.9 % / Rpim(I) all: 0.013 / Rsym value: 0.059 / Net I/av σ(I): 69 / Net I/σ(I): 69
Reflection shellResolution: 6.1→6.2 Å / Redundancy: 23.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 763 / CC1/2: 0.376 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 6.1→19.986 Å / SU ML: 1.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.6
RfactorNum. reflection% reflection
Rfree0.3405 1526 10.39 %
Rwork0.3138 --
obs0.3165 14682 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 6.1→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27360 0 0 0 27360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00528032
X-RAY DIFFRACTIONf_angle_d1.05638184
X-RAY DIFFRACTIONf_dihedral_angle_d15.8449240
X-RAY DIFFRACTIONf_chiral_restr0.0654680
X-RAY DIFFRACTIONf_plane_restr0.0044440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.1003-6.29120.41591430.41531196X-RAY DIFFRACTION100
6.2912-6.50860.46321450.40421192X-RAY DIFFRACTION100
6.5086-6.75950.39091120.43691215X-RAY DIFFRACTION100
6.7595-7.05420.39931570.41511191X-RAY DIFFRACTION100
7.0542-7.40810.4051170.39961197X-RAY DIFFRACTION100
7.4081-7.84570.35661590.33831179X-RAY DIFFRACTION100
7.8457-8.40930.33281130.31691225X-RAY DIFFRACTION100
8.4093-9.18030.24671420.25661185X-RAY DIFFRACTION100
9.1803-10.34440.28511560.25891193X-RAY DIFFRACTION100
10.3444-12.4810.29281360.26411179X-RAY DIFFRACTION98
12.481-19.98580.43181460.36571204X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.26752.14561.43465.9909-1.56992.59450.4179-0.19740.5748-1.3303-0.7-0.5210.81410.2781-0.00746.70380.4718-0.43055.7703-0.55155.603540.8007105.6545127.6103
25.67992.65780.71694.3966-0.87843.7459-0.5243-1.0405-0.0885-0.8948-0.045-0.0914-0.097-0.642-0.00115.69340.4499-0.03736.0380.30945.844183.2505141.7678121.2993
33.91330.9717-3.88881.6892-1.33737.59680.30650.28450.52220.55960.8363-0.33611.0671-0.30720.02635.7481-0.56270.0366.52321.0357.6405106.5078182.985649.8505
48.41561.3106-0.62492.60930.86196.563-0.3570.0934-1.1408-1.2384-0.29960.2992-0.4429-1.2312-0.19165.58120.13020.81035.38460.54578.3952140.7707188.541994.3141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' or chain 'B' or chain 'C' or chain 'D' or chain 'E' or chain 'F'
2X-RAY DIFFRACTION2chain 'G' or chain 'H' or chain 'I' or chain 'J' or chain 'K' or chain 'L'
3X-RAY DIFFRACTION3chain 'M' or chain 'N' or chain 'O' or chain 'P' or chain 'Q' or chain 'R'
4X-RAY DIFFRACTION4chain 'S' or chain 'T' or chain 'U' or chain 'V' or chain 'W' or chain 'X'

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