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- PDB-6iz4: Crystal Structure Analysis of TRIC counter-ion channels in calciu... -

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Basic information

Entry
Database: PDB / ID: 6iz4
TitleCrystal Structure Analysis 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: 3.098 Å
AuthorsWang, X.H. / Zeng, Y. / Gao, F. / Su, M. / Hendrickson, W.A. / 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

Downloads & links

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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
E: Trimeric intracellular cation channel type B-B
F: Trimeric intracellular cation channel type B-B
G: Trimeric intracellular cation channel type B-B
H: Trimeric intracellular cation channel type B-B
I: Trimeric intracellular cation channel type B-B
J: Trimeric intracellular cation channel type B-B
K: Trimeric intracellular cation channel type B-B
L: Trimeric intracellular cation channel type B-B


Theoretical massNumber of molelcules
Total (without water)425,56612
Polymers425,56612
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 area4850 Å2
ΔGint-52 kcal/mol
Surface area31620 Å2
MethodPISA
2
D: Trimeric intracellular cation channel type B-B
E: Trimeric intracellular cation channel type B-B
F: 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 area4850 Å2
ΔGint-51 kcal/mol
Surface area31710 Å2
MethodPISA
3
G: Trimeric intracellular cation channel type B-B
H: Trimeric intracellular cation channel type B-B
I: 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 area4840 Å2
ΔGint-52 kcal/mol
Surface area31690 Å2
MethodPISA
4
J: Trimeric intracellular cation channel type B-B
K: Trimeric intracellular cation channel type B-B
L: 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 area4850 Å2
ΔGint-52 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)290.246, 290.246, 195.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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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.: 12
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: 4.84 Å3/Da / Density % sol: 74.61 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 400, 50mM MgCl2, 100mM Glycine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.098→49.932 Å / Num. obs: 137600 / % possible obs: 91 % / Redundancy: 35.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.389 / Rpim(I) all: 0.065 / Rrim(I) all: 0.394 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.1536.64.77473910.4630.7924.84199.5
16.97-49.9327.60.0410280.9990.0080.0495.8

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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: 3.098→49.932 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3005 6778 4.94 %
Rwork0.2826 130373 -
obs0.2834 137151 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.99 Å2 / Biso mean: 75.0246 Å2 / Biso min: 23.8 Å2
Refinement stepCycle: final / Resolution: 3.098→49.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21192 0 0 0 21192
Num. residues----2688
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0976-3.13280.44462390.40924678491799
3.1328-3.16960.37442160.396747534969100
3.1696-3.20830.39152690.376747325001100
3.2083-3.24890.41382770.372446634940100
3.2489-3.29160.38712520.364547394991100
3.2916-3.33670.35722690.349347244993100
3.3367-3.38440.37452370.356247224959100
3.3844-3.43490.39861110.37082371248297
3.4349-3.48860.3825840.36541744182893
3.4886-3.54570.36422450.357647444989100
3.5457-3.60690.38362570.346647274984100
3.6069-3.67240.36291410.34682389253098
3.6724-3.7430.33571320.34222939307197
3.743-3.81940.34182770.324447345011100
3.8194-3.90240.33611420.31552936307898
3.9024-3.99320.32641640.29413351351597
3.9932-4.0930.29812490.272947464995100
4.093-4.20360.29872570.258247485005100
4.2036-4.32720.30492460.261247945040100
4.3272-4.46680.2782530.242247705023100
4.4668-4.62630.24442690.236747174986100
4.6263-4.81140.30252490.251347905039100
4.8114-5.03020.28732410.251548155056100
5.0302-5.29510.2852390.257348215060100
5.2951-5.62650.29482090.265648215030100
5.6265-6.06020.30382430.28148405083100
6.0602-6.66880.29662700.262148135083100
6.6688-7.63090.27572450.256748935138100
7.6309-9.60290.17512460.193949215167100
9.6029-49.9380.26982500.29374938518896

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