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- PDB-5dqq: Structure, inhibition and regulation of two-pore channel TPC1 fro... -

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Basic information

Entry
Database: PDB / ID: 5dqq
TitleStructure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana
ComponentsTwo pore calcium channel protein 1
KeywordsTRANSPORT PROTEIN/INHIBITOR / membrane protein / ion channel / calcium channel / sodium channel / phosphorylation dependent ion channel / asymmetric ion channel / tandem pore-forming domains / EF-hand domain / N-terminal domain / C-terminal domain / calcium sensors / voltage sensor / selectivity filter / pore gate / TRANSPORT PROTEIN-INHIBITOR complex
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
trans-Ned 19 / PALMITIC ACID / Two pore calcium channel protein 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.872 Å
AuthorsKintzer, A.F. / Stroud, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
CitationJournal: Nature / Year: 2016
Title: Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana
Authors: Kintzer, A.F. / Stroud, R.M.
History
DepositionSep 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 13, 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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_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_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)84,89510
Polymers83,8441
Non-polymers1,0529
Water1,02757
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)169,79020
Polymers167,6872
Non-polymers2,10318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10370 Å2
ΔGint-176 kcal/mol
Surface area69930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.180, 154.810, 219.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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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: 83843.625 Da / Num. of mol.: 1 / Fragment: UNP residues 12-733, EF-hand Helix 4
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: p423_GAL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DSY-5 / References: UniProt: Q94KI8
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical ChemComp-66R / trans-Ned 19 / (1R,3S)-1-(3-{[4-(2-fluorophenyl)piperazin-1-yl]methyl}-4-methoxyphenyl)-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxy lic acid


Mass: 514.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C30H31FN4O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 4.41 Å3/Da / Density % sol: 72.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: 0.1 M glycine, pH 9.3, 50 mM potassium chloride, 1 mM calcium chloride, 35% PEG300
PH range: 9.0-9.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.111, 1.006, 1.25465, 1.3854, 1.75
SYNCHROTRONALS 5.0.22
SYNCHROTRONSSRL BL12-23
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 24, 2015
ADSC QUANTUM 315r2CCD
DECTRIS PILATUS 6M3PIXEL
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2double crystal Si(111)SINGLE WAVELENGTHMx-ray1
3double crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.0061
31.254651
41.38541
51.751
ReflectionNumber: 431212 / Rmerge(I) obs: 0.281 / Χ2: 0.95 / D res high: 3.5 Å / Num. obs: 19817 / % possible obs: 97.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
2020.9441410.09
152016410.093
121527110.101
101238110.095
91034010.11
8951910.152
7884310.228
67151310.466
5.56118310.66
55.5172410.58
45643311.145
3.54643214.267
ReflectionResolution: 2.7→109.885 Å / Num. all: 36476 / Num. obs: 21275 / % possible obs: 93.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 108 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.156 / Χ2: 1.005 / Net I/σ(I): 10.42 / Num. measured all: 287001
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-37.30.2740.7320.31671461113090567.32881.4
3-3.50.8911.2291.688231411151110221.3298.8
3.5-40.9870.3775.9446216629662250.40598.9
4-4.50.9960.17512.6227580382037600.18998.4
4.5-50.9990.08720.2817586246424230.09398.3
5-60.9990.07323.6719862280527850.07999.3
6-70.9990.05630.399886144014380.0699.9
7-80.9990.03345.7657738218170.03699.5
8-910.02560.4134665025020.027100
9-1010.0269.1321903223200.02299.4
10-1510.0269.1640516286200.02298.7
15-2010.01968.418801551460.02194.2
20-20.9440.9990.02266.295112890.0257

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Phasing

PhasingMethod: MIRAS
Phasing set
ID
1
2
3
4
5
Phasing MIRResolution: 3.5→20.96 Å / FOM acentric: 0.229 / FOM centric: 0.298 / Reflection acentric: 16868 / Reflection centric: 2048
Phasing MIR der

Native set-ID: 1 / Resolution: 3.5→20.96 Å

IDDer set-IDPower acentricPower centricReflection acentricReflection centric
ISO_1100166862008
ISO_221.140.903118891590
ISO_332.3322.08862281031
ISO_441.1911.37110341543
ISO_550.7260.608121301612
Phasing MIR der shell
Highest resolution (Å)Lowest resolution (Å)Der-IDPower acentricPower centricReflection acentricReflection centric
12.6620.96ISO_100264104
9.912.66ISO_100390106
8.49.9ISO_100480105
7.428.4ISO_10057797
6.727.42ISO_100634110
6.196.72ISO_100704105
5.776.19ISO_100761100
5.425.77ISO_100808108
5.135.42ISO_100875105
4.885.13ISO_100900101
4.674.88ISO_100959108
4.484.67ISO_100100793
4.314.48ISO_1001044115
4.164.31ISO_1001075103
4.024.16ISO_100112398
3.94.02ISO_10090093
3.793.9ISO_1001192104
3.683.79ISO_10085567
3.593.68ISO_10084177
3.53.59ISO_1001297109
12.6620.96ISO_21.7011.333263104
9.912.66ISO_21.290.696390106
8.49.9ISO_21.2140.817480105
7.428.4ISO_21.2410.96157797
6.727.42ISO_21.2690.897634110
6.196.72ISO_21.0650.827704105
5.776.19ISO_20.8770.585761100
5.425.77ISO_20.6280.569808108
5.135.42ISO_20.4740.395873105
4.885.13ISO_20.3420.324897101
4.674.88ISO_20.2340.183958108
4.484.67ISO_20.1580.149100593
4.314.48ISO_20.1030.081043115
4.164.31ISO_20.0460.0391072103
4.024.16ISO_20.0180.015112098
3.94.02ISO_20.0490.04130432
3.793.9ISO_20000
3.683.79ISO_20000
3.593.68ISO_20000
3.53.59ISO_20000
12.6620.96ISO_34.9713.33259101
9.912.66ISO_33.231.93390106
8.49.9ISO_32.781.944479105
7.428.4ISO_32.4812.10957797
6.727.42ISO_32.0241.824634110
6.196.72ISO_31.5421.175704105
5.776.19ISO_31.1630.974759100
5.425.77ISO_30.7070.673796107
5.135.42ISO_30.3790.296859104
4.885.13ISO_30.1940.16774586
4.674.88ISO_30.0860.1672610
4.484.67ISO_30000
4.314.48ISO_30000
4.164.31ISO_30000
4.024.16ISO_30000
3.94.02ISO_30000
3.793.9ISO_30000
3.683.79ISO_30000
3.593.68ISO_30000
3.53.59ISO_30000
12.6620.96ISO_44.1732.497261102
9.912.66ISO_43.5072.455390106
8.49.9ISO_42.9722.05480104
7.428.4ISO_42.1771.59957797
6.727.42ISO_41.6251.147633110
6.196.72ISO_41.0780.929700105
5.776.19ISO_40.6740.573760100
5.425.77ISO_40.4670.35803108
5.135.42ISO_40.3090.234869105
4.885.13ISO_40.2020.189895101
4.674.88ISO_40.090.062950108
4.484.67ISO_40.0580.05390789
4.314.48ISO_40.0150.016993111
4.164.31ISO_40.0060.00593992
4.024.16ISO_40.0030.00254169
3.94.02ISO_40.0050.00433636
3.793.9ISO_40000
3.683.79ISO_40000
3.593.68ISO_40000
3.53.59ISO_40000
12.6620.96ISO_50.9110.761261103
9.912.66ISO_50.7380.512390106
8.49.9ISO_50.7540.587480105
7.428.4ISO_50.8170.62957797
6.727.42ISO_50.9640.633634110
6.196.72ISO_50.9370.643704105
5.776.19ISO_50.9730.69761100
5.425.77ISO_50.8840.751808108
5.135.42ISO_50.8120.663874105
4.885.13ISO_50.6880.561899100
4.674.88ISO_50.5420.478956108
4.484.67ISO_50.5180.457100593
4.314.48ISO_50.5080.4391042115
4.164.31ISO_50.4670.4141049102
4.024.16ISO_50.5630.475110898
3.94.02ISO_50.3770.39157456
3.793.9ISO_50.240.38381
3.683.79ISO_50000
3.593.68ISO_50000
3.53.59ISO_50000
Phasing MIR shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
12.66-20.960.9560.902264104
9.9-12.660.9060.742390107
8.4-9.90.8440.705480105
7.42-8.40.7540.614577100
6.72-7.420.5860.55639111
6.19-6.720.4580.462704106
5.77-6.190.3590.368763101
5.42-5.770.2990.244814112
5.13-5.420.240.219877105
4.88-5.130.2080.201930106
4.67-4.880.1780.225972109
4.48-4.670.1530.155102199
4.31-4.480.1250.1641062119
4.16-4.310.1180.0941093104
4.02-4.160.1030.0691132101
3.9-4.020.0890.057965102
3.79-3.90.0010.0011192104
3.68-3.790085567
3.59-3.680084177
3.5-3.59001297109

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Processing

Software
NameClassification
PHENIXrefinement
SHARPphasing
DMphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.872→38.703 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3394 1052 4.95 %
Rwork0.297 20218 -
obs0.299 21270 61.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 368.39 Å2 / Biso mean: 110.3123 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 2.872→38.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 63 57 5402
Biso mean--123.16 75.8 -
Num. residues----649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045472
X-RAY DIFFRACTIONf_angle_d0.7447432
X-RAY DIFFRACTIONf_chiral_restr0.04842
X-RAY DIFFRACTIONf_plane_restr0.004914
X-RAY DIFFRACTIONf_dihedral_angle_d17.6993156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8723-3.0030.800980.64982042125
3.003-3.16120.5912270.526559962615
3.1612-3.35920.3716550.40341251130631
3.3592-3.61840.39571270.35242369249658
3.6184-3.98210.3641820.30433399358183
3.9821-4.55760.34142140.2714058427299
4.5576-5.73910.30432160.28134111432799
5.7391-38.7060.32152230.28774227445098
Refinement TLS params.Method: refined / Origin x: -25.0661 Å / Origin y: -12.366 Å / Origin z: 15.5844 Å
111213212223313233
T0.185 Å2-0.1934 Å2-0.246 Å2-0.0821 Å2-0.4493 Å2---0.0025 Å2
L2.0249 °20.0265 °20.59 °2-0.774 °2-0.2781 °2--0.7621 °2
S0.4383 Å °-1.0496 Å °-0.7877 Å °0.4388 Å °-0.0975 Å °0.0856 Å °0.0267 Å °-0.2541 Å °2.3682 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA30 - 810
2X-RAY DIFFRACTION1allB3 - 80
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1

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