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

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Basic information

Entry
Database: PDB / ID: 6iyz
TitleStructural basis for activity of TRIC counter-ion channels in calcium release
ComponentsTrimeric intracellular cation channel type A
KeywordsMEMBRANE PROTEIN / TRIC / cation channel
Function / homologyTRIC channel / TRIC channel / regulation of release of sequestered calcium ion into cytosol / potassium channel activity / sarcoplasmic reticulum membrane / nuclear membrane / identical protein binding / Trimeric intracellular cation channel type A
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, X.H. / Zeng, Y. / Qin, L. / Gao, F. / 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0283
Polymers36,9581
Non-polymers712
Water23413
1
A: Trimeric intracellular cation channel type A
hetero molecules

A: Trimeric intracellular cation channel type A
hetero molecules

A: Trimeric intracellular cation channel type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0859
Polymers110,8733
Non-polymers2136
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation54_555z,-x,-y1
Buried area5650 Å2
ΔGint-67 kcal/mol
Surface area30620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.210, 268.210, 268.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-401-

CL

21A-502-

HOH

31A-512-

HOH

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Components

#1: Protein Trimeric intracellular cation channel type A / TRICA / Transmembrane protein 38A


Mass: 36957.551 Da / Num. of mol.: 1 / Mutation: C245S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TMEM38A, RCJMB04_13f15 / Production host: Schizosaccharomyces (fungus) / References: UniProt: Q5ZK43
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 5.44 Å3/Da / Density % sol: 77.38 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: NaH2PO4, K2HPO4, phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→47.41 Å / Num. obs: 42420 / % possible obs: 100 % / Redundancy: 147.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.392 / Rpim(I) all: 0.032 / Rrim(I) all: 0.394 / Net I/σ(I): 24.3 / Num. measured all: 6242648 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.27150.818.65854417136080.4651.51618.7211.199.8
9.07-47.41109.30.065801497330.9990.0060.06610799.4

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
Aimless0.5.29data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IYU

6iyu


Resolution: 2.2→47.413 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 2199 5.19 %
Rwork0.2509 40169 -
obs0.2522 42368 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.89 Å2 / Biso mean: 60.6597 Å2 / Biso min: 33.02 Å2
Refinement stepCycle: final / Resolution: 2.2→47.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 2 13 1811
Biso mean--84.58 53.01 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1996-2.24750.39651130.368625002613
2.2475-2.29970.32761390.325224382577
2.2997-2.35720.36481430.3124512594
2.3572-2.4210.32521330.29824782611
2.421-2.49220.27911360.293224502586
2.4922-2.57260.28311260.288624792605
2.5726-2.66460.3211260.276624922618
2.6646-2.77130.31061350.269124852620
2.7713-2.89740.26751340.247124822616
2.8974-3.05010.22481260.24125072633
3.0501-3.24120.2771510.255424972648
3.2412-3.49130.26791390.234125012640
3.4913-3.84250.24281330.225625342667
3.8425-4.39820.22541370.216225572694
4.3982-5.53990.26471520.227625762728
5.5399-47.42430.30321760.27627422918

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