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- PDB-6iz1: Crystal Structure Analysis of a Eukaryotic Membrane Protein -

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Basic information

Entry
Database: PDB / ID: 6iz1
TitleCrystal Structure Analysis of a Eukaryotic Membrane Protein
ComponentsTrimeric intracellular cation channel type A
KeywordsMEMBRANE PROTEIN / TRIC / cation channel
Function / homologyTRIC channel / TRIC channel / 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: 2.399 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)37,1747
Polymers36,9571
Non-polymers2176
Water1,29772
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)111,52221
Polymers110,8703
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-222 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.348, 127.348, 101.801
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-516-

HOH

31A-543-

HOH

41A-553-

HOH

51A-571-

HOH

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Components

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


Mass: 36956.500 Da / Num. of mol.: 1 / Mutation: K129Q/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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.22 Å3/Da / Density % sol: 61.85 %
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: May 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→48.49 Å / Num. obs: 17876 / % possible obs: 90.9 % / Redundancy: 38.5 % / CC1/2: 1 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.023 / Rrim(I) all: 0.142 / Net I/σ(I): 23.1 / Num. measured all: 688445
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
2.4-2.4940.55.4548085719960.4820.8585.5221.199.9
8.97-48.4929.40.0351345345710.0070.035108.299.4

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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: 2.399→48.487 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 906 5.08 %
Rwork0.2169 16932 -
obs0.2187 17838 90.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.35 Å2 / Biso mean: 75.9211 Å2 / Biso min: 45.83 Å2
Refinement stepCycle: final / Resolution: 2.399→48.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 6 72 1874
Biso mean--59.89 78.06 -
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3988-2.54910.33661590.300630273186100
2.5491-2.74590.33251300.26552111224170
2.7459-3.02220.24891680.19730563224100
3.0222-3.45940.19491630.175427932956100
3.4594-4.35810.21391400.18112615275585
4.3581-48.49670.28661460.235533303476100
Refinement TLS params.Method: refined / Origin x: 45.1576 Å / Origin y: 29.6093 Å / Origin z: 43.8502 Å
111213212223313233
T0.4174 Å2-0.0569 Å20.0854 Å2-0.4872 Å20.035 Å2--0.5971 Å2
L2.2116 °2-0.6429 °2-0.6165 °2-1.603 °20.5652 °2--1.7741 °2
S-0.0531 Å °-0.1067 Å °-0.3387 Å °0.1758 Å °-0.0778 Å °0.3784 Å °0.2117 Å °-0.2457 Å °0.1555 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 - 105

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