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- PDB-5tua: structure of a Na+-selective mutant of two-pore channel from Arab... -

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Basic information

Entry
Database: PDB / ID: 5tua
Titlestructure of a Na+-selective mutant of two-pore channel from Arabidopsis thaliana AtTPC1
ComponentsTwo pore calcium channel protein 1
Keywordsmetal transport / membrane protein / two-pore channel / Na+-selective
Function / homology
Function and homology information


regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport ...regulation of jasmonic acid biosynthetic process / seed germination / regulation of stomatal movement / plant-type vacuole / vacuole / vacuolar membrane / monoatomic ion channel complex / voltage-gated calcium channel activity / calcium-mediated signaling / calcium ion transport / calcium ion binding / Golgi apparatus / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Two pore calcium channel protein 1, plant / Voltage-dependent channel domain superfamily / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / Two pore calcium channel protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuo, J. / Zeng, W. / Jiang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Tuning the ion selectivity of two-pore channels.
Authors: Guo, J. / Zeng, W. / Jiang, Y.
History
DepositionNov 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_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

Downloads & links

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Assembly

Deposited unit
A: Two pore calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,81813
Polymers85,4781
Non-polymers1,33912
Water0
1
A: Two pore calcium channel protein 1
hetero molecules

A: Two pore calcium channel protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,63526
Polymers170,9572
Non-polymers2,67824
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9590 Å2
ΔGint-168 kcal/mol
Surface area66780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.535, 156.371, 217.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-805-

BA

21A-810-

BA

31A-811-

BA

41A-812-

NA

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Components

#1: Protein Two pore calcium channel protein 1 / Calcium channel protein 1 / AtCCH1 / Fatty acid oxygenation up-regulated protein 2 / Voltage- ...Calcium channel protein 1 / AtCCH1 / Fatty acid oxygenation up-regulated protein 2 / Voltage-dependent calcium channel protein TPC1 / AtTPC1


Mass: 85478.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPC1, CCH1, FOU2, At4g03560, F9H3.19, T5L23.5 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q94KI8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 4.4 Å3/Da / Density % sol: 72.02 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 24-26% PEG400, 100-150 mM BaCl2, 100 mM HEPES pH7.0 or 100 mM MES pH6.0
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 20921 / % possible obs: 90.3 % / Redundancy: 5.7 % / Net I/σ(I): 17.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e1j

5e1j


Resolution: 3.3→44.589 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.35
RfactorNum. reflection% reflection
Rfree0.3229 727 4.97 %
Rwork0.3103 --
obs0.3109 14620 62.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→44.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 12 0 5126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095254
X-RAY DIFFRACTIONf_angle_d0.8667128
X-RAY DIFFRACTIONf_dihedral_angle_d16.4923038
X-RAY DIFFRACTIONf_chiral_restr0.044820
X-RAY DIFFRACTIONf_plane_restr0.007878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2903-3.54420.4806330.3228632X-RAY DIFFRACTION15
3.5442-3.90070.3027740.31291344X-RAY DIFFRACTION31
3.9007-4.46470.31351710.30573256X-RAY DIFFRACTION74
4.4647-5.62330.32372230.30234303X-RAY DIFFRACTION97
5.6233-44.59330.31832260.31894358X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1775-0.5183-1.23021.7466-0.69792.2892-0.0030.0960.45260.2381-0.1776-0.21770.2655-0.41340.14330.6388-0.2291-0.16821.20580.25941.19778.3939-25.500525.9798
22.0921-0.3123-0.0750.26090.40350.79370.1634-0.3526-0.9310.29590.1882-0.36410.50150.07890.5146-0.00770.28540.06330.2923-0.50820.63331.4808-19.28742.8019
33.49081.0846-0.19953.3331-1.83632.36660.4018-1.5529-0.41380.84060.03161.06210.0683-0.8437-0.10620.3158-0.2645-0.18331.0631-0.14210.6622-10.3446-13.741418.853
40.7245-0.1670.65010.43250.07421.47450.0624-0.4192-0.05120.3187-0.0654-0.12760.0647-0.22620.00640.7352-0.2551-0.49481.1914-0.27580.509521.3281-0.440937.9197
50.19560.11650.10290.30710.17280.25210.0411-0.0318-0.0950.05650.0277-0.29950.12310.1554-0.1813-0.28940.0741-0.21590.1617-0.4680.268630.9613-9.76246.4752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 295 )
3X-RAY DIFFRACTION3chain 'A' and (resid 296 through 398 )
4X-RAY DIFFRACTION4chain 'A' and (resid 399 through 547 )
5X-RAY DIFFRACTION5chain 'A' and (resid 548 through 686 )

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