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- PDB-6iz0: Crystal Structure Analysis of a Eukaryotic Membrane Protein -

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Basic information

Entry
Database: PDB / ID: 6iz0
TitleCrystal Structure Analysis of a Eukaryotic Membrane Protein
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: 2.3 Å
AuthorsWang, X.H. / Zeng, Y. / 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)37,1177
Polymers36,8991
Non-polymers2176
Water86548
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)111,35021
Polymers110,6983
Non-polymers65218
Water543
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 area7660 Å2
ΔGint-221 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.049, 127.049, 101.448
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-401-

CA

21A-518-

HOH

31A-538-

HOH

41A-539-

HOH

51A-547-

HOH

61A-548-

HOH

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Components

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


Mass: 36899.449 Da / Num. of mol.: 1 / Mutation: K129A/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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.2 Å3/Da / Density % sol: 61.59 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→41.59 Å / Num. obs: 24924 / % possible obs: 99.6 % / Redundancy: 40.2 % / CC1/2: 1 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.03 / Rrim(I) all: 0.191 / Net I/σ(I): 23.9 / Num. measured all: 1001482
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.2736.56.75420290.3591.1136.84896.1
9.08-41.5931.90.02341710.0040.02496.6

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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: 6IYU

6iyu


Resolution: 2.3→41.587 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.43
RfactorNum. reflection% reflection
Rfree0.2397 1121 5.11 %
Rwork0.2188 --
obs0.2198 21925 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.43 Å2 / Biso mean: 64.4219 Å2 / Biso min: 32.73 Å2
Refinement stepCycle: final / Resolution: 2.3→41.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 6 48 1846
Biso mean--52.65 59.33 -
Num. residues----224
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 (%)
2.3-2.40470.36081340.292525512685100
2.4047-2.53150.30821410.269225482689100
2.5315-2.69010.24761510.245525482699100
2.6901-2.89770.25151440.216525672711100
2.8977-3.18920.22971360.205825802716100
3.1892-3.65050.18571480.202325692717100
3.6505-4.59830.22151480.20132622277099
4.5983-41.59330.26021190.22432819293899
Refinement TLS params.Method: refined / Origin x: 44.9209 Å / Origin y: 29.4222 Å / Origin z: 43.8152 Å
111213212223313233
T0.3597 Å2-0.0408 Å20.1188 Å2-0.4574 Å20.0079 Å2--0.5276 Å2
L2.2475 °2-0.2923 °2-0.4089 °2-1.5455 °20.0102 °2--1.7964 °2
S-0.0721 Å °-0.2772 Å °-0.2392 Å °0.271 Å °-0.0848 Å °0.4962 Å °0.2176 Å °-0.4654 Å °0.1612 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 231
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allD1 - 5
4X-RAY DIFFRACTION1allS1 - 48

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