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- PDB-5e1j: Structure of voltage-gated two-pore channel TPC1 from Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 5e1j
TitleStructure of voltage-gated two-pore channel TPC1 from Arabidopsis thaliana
ComponentsTwo pore calcium channel protein 1
KeywordsMETAL TRANSPORT / two-pore channel / voltage-gated / calcium modulation
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. / EF-hand domain / Ion transport domain / Ion transport protein / 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 / SIRAS / Resolution: 3.308 Å
AuthorsGuo, J. / Zeng, W. / Chen, Q. / Lee, C. / Chen, L. / Yang, Y. / Jiang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationI-1578 United States
CitationJournal: Nature / Year: 2016
Title: Structure of the voltage-gated two-pore channel TPC1 from Arabidopsis thaliana.
Authors: Guo, J. / Zeng, W. / Chen, Q. / Lee, C. / Chen, L. / Yang, Y. / Cang, C. / Ren, D. / Jiang, Y.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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

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)86,90311
Polymers85,7241
Non-polymers1,17910
Water724
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)173,80522
Polymers171,4472
Non-polymers2,35820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9680 Å2
ΔGint-176 kcal/mol
Surface area66250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.430, 158.850, 217.240
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-801-

BA

21A-803-

BA

31A-904-

HOH

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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: 85723.742 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 / Plasmid: pPICZ / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1163 / References: UniProt: Q94KI8
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.58 Å3/Da / Density % sol: 73.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26% PEG400, 150 mM BaCl2, 100mM HEPES / PH range: 5.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: 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: 34119 / % possible obs: 96.2 % / Redundancy: 6.5 % / Rsym value: 0.06 / Net I/σ(I): 36.1
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.6 / % possible all: 78.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.308→39.712 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 36.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3321 1741 5.1 %Random selection
Rwork0.3247 ---
obs0.3251 22635 77.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.15 Å2
Refinement stepCycle: LAST / Resolution: 3.308→39.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4949 0 10 4 4963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065097
X-RAY DIFFRACTIONf_angle_d0.8546894
X-RAY DIFFRACTIONf_dihedral_angle_d11.6811758
X-RAY DIFFRACTIONf_chiral_restr0.03803
X-RAY DIFFRACTIONf_plane_restr0.005849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.308-3.40550.357140.3768331X-RAY DIFFRACTION9
3.4055-3.51540.3778560.3841970X-RAY DIFFRACTION28
3.5154-3.64090.4133800.3751734X-RAY DIFFRACTION49
3.6409-3.78660.35331240.36322334X-RAY DIFFRACTION66
3.7866-3.95880.3361650.36092874X-RAY DIFFRACTION83
3.9588-4.16730.29871880.353354X-RAY DIFFRACTION97
4.1673-4.4280.26921950.32363485X-RAY DIFFRACTION100
4.428-4.76940.32572040.28953463X-RAY DIFFRACTION100
4.7694-5.24840.33441810.30613480X-RAY DIFFRACTION100
5.2484-6.00560.34871830.37483496X-RAY DIFFRACTION100
6.0056-7.55790.40141780.35223518X-RAY DIFFRACTION100
7.5579-39.71530.3111730.27413339X-RAY DIFFRACTION96
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)
11.8221-0.9697-0.41880.78250.38080.19030.2559-1.2094-1.48290.3226-0.3980.11990.3121-0.05070.11840.6668-0.1187-0.05272.04190.62791.8308-34.5956-25.078226.0597
23.00250.01980.03551.28350.06051.20870.314-0.5767-1.12420.26910.0045-0.14410.4323-0.2139-0.04820.41750.0645-0.1590.5105-0.2070.742-27.5427-17.27538.253
30.22730.02760.26850.3959-0.05261.11040.1712-0.3113-0.13390.3821-0.0295-0.18920.1561-0.1691-0.0930.9684-0.3414-0.38941.4557-0.30840.6085-21.77580.212137.7422
40.54030.3850.20341.16030.04630.93490.0847-0.164-0.08880.120.094-0.6370.13180.3367-0.34160.24970.0548-0.18430.4432-0.36870.5208-13.5933-9.62066.3042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 32:91 )A32 - 91
2X-RAY DIFFRACTION2( CHAIN A AND RESID 92:398 )A92 - 398
3X-RAY DIFFRACTION3( CHAIN A AND RESID 399:547 )A399 - 547
4X-RAY DIFFRACTION4( CHAIN A AND RESID 548:686 )A548 - 686

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