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- PDB-6bbf: The CRAC channel Orai in an open conformation; H206A gain-of-func... -

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Basic information

Entry
Database: PDB / ID: 6bbf
TitleThe CRAC channel Orai in an open conformation; H206A gain-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 / Resolution: 6.706 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 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Aug 16, 2023Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible

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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)579,84424
Polymers579,84424
Non-polymers00
Water0
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


  • defined by author&software
  • Evidence: light scattering
  • 145 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)144,9616
Polymers144,9616
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15460 Å2
ΔGint-245 kcal/mol
Surface area53110 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


  • defined by author&software
  • 145 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)144,9616
Polymers144,9616
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15600 Å2
ΔGint-247 kcal/mol
Surface area52970 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


  • defined by author&software
  • 145 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)144,9616
Polymers144,9616
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15630 Å2
ΔGint-247 kcal/mol
Surface area53190 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


  • defined by author&software
  • 145 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)144,9616
Polymers144,9616
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-252 kcal/mol
Surface area52510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.344, 262.344, 220.443
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: 24160.168 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 38% PEG 400 500 mM NaCl 100 mM Tris-HCl / PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 6.7→50 Å / Num. obs: 13366 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 55.8 % / Rpim(I) all: 0.011 / Rsym value: 0.083 / Net I/σ(I): 92.4
Reflection shellResolution: 6.7→6.82 Å / Redundancy: 58.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 644 / CC1/2: 0.214 / Rpim(I) all: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 6.706→19.982 Å / SU ML: 1.91 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 46.72
RfactorNum. reflection% reflection
Rfree0.337 1300 10.12 %
Rwork0.3121 --
obs0.3145 12844 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 6.706→19.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27120 0 0 0 27120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627720
X-RAY DIFFRACTIONf_angle_d1.16337704
X-RAY DIFFRACTIONf_dihedral_angle_d16.2249240
X-RAY DIFFRACTIONf_chiral_restr0.0714680
X-RAY DIFFRACTIONf_plane_restr0.0054392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.7064-6.96390.50881350.41591230X-RAY DIFFRACTION96
6.9639-7.26630.44481350.42181298X-RAY DIFFRACTION100
7.2663-7.62910.4651560.41991258X-RAY DIFFRACTION100
7.6291-8.07730.37371360.37231294X-RAY DIFFRACTION100
8.0773-8.65360.36481530.331288X-RAY DIFFRACTION100
8.6536-9.44010.23581440.24321304X-RAY DIFFRACTION100
9.4401-10.62270.28821480.24881283X-RAY DIFFRACTION100
10.6227-12.77370.29151550.29691284X-RAY DIFFRACTION99
12.7737-19.98210.39131380.3461305X-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)
15.4243-0.4949-1.618810.78820.36852.05781.1186-0.0822-0.13082.768-2.3656-3.394-0.49841.1569-0.83116.2519-1.4049-1.16487.74641.97336.6028112.485386.8846.175
27.7139-2.5923.723110.503-3.947414.18932.07360.734-1.50430.0207-0.4439-0.5959-0.30440.65620.58286.22070.26860.59045.961-0.85597.480363.7229148.212675.0665
39.4411-4.80793.68217.1072-0.73356.9262-2.41873.63782.67973.276-1.3914-1.163-1.78212.3683-1.41337.7801-2.0662-0.51176.45981.57916.7975149.514444.807240.0262
45.4058-4.330.135811.903-3.5615.39971.78880.09710.62730.8384-1.13595.69320.05281.9814-0.37347.38190.3831-0.54586.6272-2.11729.027766.6885113.8696120.9533
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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