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

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Basic information

Entry
Database: PDB / ID: 6izf
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 / Chem-BQ9 / Trimeric intracellular cation channel type A
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, X.H. / Zeng, Y. / 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 19, 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)37,6548
Polymers36,9581
Non-polymers6967
Water1,56787
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)112,96124
Polymers110,8733
Non-polymers2,08821
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 area8880 Å2
ΔGint-230 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.381, 127.381, 102.167
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-521-

HOH

31A-545-

HOH

41A-557-

HOH

51A-586-

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-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: Chemical ChemComp-BQ9 / (2R)-1-(dodecanoyloxy)-3-hydroxypropan-2-yl (5E,8E,11E)-tetradeca-5,8,11-trienoate


Mass: 478.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H50O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.24 Å3/Da / Density % sol: 62 %
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: APS / Beamline: 24-ID-C / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.99→48.54 Å / Num. obs: 33712 / % possible obs: 99.6 % / Redundancy: 234.6 % / CC1/2: 1 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.015 / Rrim(I) all: 0.236 / Net I/σ(I): 32.1 / Num. measured all: 7908350 / Scaling rejects: 476
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.99-2.05121.52.21824480.4230.1912.22695.4
8.69-48.54239.30.08850010.0060.08899.5

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Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
Aimless0.5.28data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IYU

6iyu


Resolution: 2→14.992 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.12
RfactorNum. reflection% reflection
Rfree0.2053 1681 5.03 %
Rwork0.1837 --
obs0.1848 33422 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.47 Å2 / Biso mean: 52.9376 Å2 / Biso min: 23.38 Å2
Refinement stepCycle: final / Resolution: 2→14.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 40 87 1923
Biso mean--81.59 56.49 -
Num. residues----224
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.05870.39541400.365125982738
2.0587-2.1250.25571220.225126102732
2.125-2.20070.23041330.198226062739
2.2007-2.28860.17911320.183826002732
2.2886-2.39230.21511430.180226042747
2.3923-2.51790.23491430.175826172760
2.5179-2.67480.21551530.169226122765
2.6748-2.880.1921450.150726072752
2.88-3.16730.17161450.164226572802
3.1673-3.620.16851520.16526602812
3.62-4.53970.19871460.169926982844
4.5397-14.99210.21511270.19928722999
Refinement TLS params.Method: refined / Origin x: 45.4795 Å / Origin y: 29.4872 Å / Origin z: 43.9823 Å
111213212223313233
T0.261 Å2-0.0301 Å20.0886 Å2-0.3278 Å20.0072 Å2--0.3622 Å2
L2.0409 °2-0.4058 °2-0.6097 °2-1.4906 °2-0.0238 °2--1.3142 °2
S-0.0986 Å °-0.1998 Å °-0.2771 Å °0.2433 Å °-0.0356 Å °0.4291 Å °0.1546 Å °-0.2604 Å °0.1177 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
5X-RAY DIFFRACTION1allB1

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