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- PDB-6iz3: Structural basis for activity of TRIC counter-ion channels in cal... -

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Basic information

Entry
Database: PDB / ID: 6iz3
TitleStructural basis for activity of TRIC counter-ion channels in calcium release
ComponentsTrimeric intracellular cation channel type B-B
KeywordsMEMBRANE PROTEIN
Function / homologyTRIC channel / TRIC channel / regulation of release of sequestered calcium ion into cytosol / potassium channel activity / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / Trimeric intracellular cation channel type B-B
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.791 Å
AuthorsZeng, Y. / Wang, X.H. / Su, M. / Chen, Y.H.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500503 China
Ministry of Science and Technology (China)2015CB910102 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Structural basis for activity of TRIC counter-ion channels in calcium release.
Authors: Wang, X.H. / Su, M. / Gao, F. / Xie, W. / Zeng, Y. / Li, D.L. / Liu, X.L. / Zhao, H. / Qin, L. / Li, F. / Liu, Q. / Clarke, O.B. / Lam, S.M. / Shui, G.H. / Hendrickson, W.A. / Chen, Y.H.
History
DepositionDec 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimeric intracellular cation channel type B-B
B: Trimeric intracellular cation channel type B-B
C: Trimeric intracellular cation channel type B-B
D: Trimeric intracellular cation channel type B-B


Theoretical massNumber of molelcules
Total (without water)141,8554
Polymers141,8554
Non-polymers00
Water00
1
A: Trimeric intracellular cation channel type B-B
B: Trimeric intracellular cation channel type B-B
C: Trimeric intracellular cation channel type B-B


Theoretical massNumber of molelcules
Total (without water)106,3923
Polymers106,3923
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-51 kcal/mol
Surface area31650 Å2
MethodPISA
2
D: Trimeric intracellular cation channel type B-B

D: Trimeric intracellular cation channel type B-B

D: Trimeric intracellular cation channel type B-B


Theoretical massNumber of molelcules
Total (without water)106,3923
Polymers106,3923
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area4830 Å2
ΔGint-52 kcal/mol
Surface area31580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.124, 190.124, 117.587
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
Trimeric intracellular cation channel type B-B / TRICB-B / Transmembrane protein 38B-B


Mass: 35463.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: tmem38b-b / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q6GN30

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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: 4.32 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, KNO3 K-Citrate PH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 3.78→47.85 Å / Num. obs: 24627 / % possible obs: 99.3 % / Redundancy: 37.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.039 / Rrim(I) all: 0.241 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.78-4.0436.67.72342960.371.2937.83496.5
10.7-47.8534.50.07911650.9990.0140.0898.9

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IZ5

6iz5


Resolution: 3.791→47.845 Å / SU ML: 0.77 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.43
RfactorNum. reflection% reflection
Rfree0.3411 1153 4.73 %
Rwork0.2993 --
obs0.3007 24398 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 311.66 Å2 / Biso mean: 200.5016 Å2 / Biso min: 127.09 Å2
Refinement stepCycle: final / Resolution: 3.791→47.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7064 0 0 0 7064
Num. residues----896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.791-3.96350.4131420.42042684282693
3.9635-4.17230.42441450.393728643009100
4.1723-4.43350.34041530.337728923045100
4.4335-4.77560.33931590.292429053064100
4.7756-5.25560.33371280.277929243052100
5.2556-6.01480.3571440.289829363080100
6.0148-7.57320.32411640.282129453109100
7.5732-47.8490.32921180.289830953213100

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