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

ID or keywords:

Entry

Database: PDB / ID: 5dqq

Title

Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana

Components

Two pore calcium channel protein 1

Keywords

TRANSPORT 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 ...
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MIRAS / Resolution: 2.872 Å

Authors

Kintzer, A.F. / Stroud, R.M.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2016
Title: Structure, inhibition and regulation of two-pore channel TPC1 from Arabidopsis thaliana
Authors: Kintzer, A.F. / Stroud, R.M.

History

Deposition	Sep 15, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Sep 13, 2017	Group: 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 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 6, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5dqq.cif.gz	295.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5dqq_validation.pdf.gz	844.9 KB	Display	wwPDB validaton report
Full document	5dqq_full_validation.pdf.gz	912.1 KB	Display
Data in XML	5dqq_validation.xml.gz	34.2 KB	Display
Data in CIF	5dqq_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dq/5dqq ftp://data.pdbj.org/pub/pdb/validation_reports/dq/5dqq	HTTPS FTP

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Related structure data

Similar structure data	5tua-1 5e1j-1 6e1n-d 6e1p-d 3gli-2 3glf-2 6nmd-d 3glg-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#243 - Mar 2020 Voltage-gated Sodium Channels similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Two pore calcium channel protein 1

hetero molecules

84.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Two pore calcium channel protein 1

hetero molecules

A: Two pore calcium channel protein 1

hetero molecules

defined by author&software
170 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁

Symmetry

Point symmetry: (Schoenflies symbol: C₂ (2 fold cyclic))

#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 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 Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.41 Å³/Da / Density % sol: 72.1 %
Crystal grow	Temperature: 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

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	ALS	8.3.1	1	1, 1.006, 1.25465, 1.3854, 1.75
SYNCHROTRON	ALS	5.0.2	2
SYNCHROTRON	SSRL	BL12-2	3

Detector

Type	ID	Detector	Date
ADSC QUANTUM 315r	1	CCD	Feb 24, 2015
ADSC QUANTUM 315r	2	CCD
DECTRIS PILATUS 6M	3	PIXEL

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	double crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	double crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1
3	double crystal Si(111)	SINGLE WAVELENGTH	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1	1
2	1.006	1
3	1.25465	1
4	1.3854	1
5	1.75	1

Reflection

Number: 431212 / R_merge(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. obs	ID	R_merge(I) obs
20	20.944	14	1	0.09
15	20	164	1	0.093
12	15	271	1	0.101
10	12	381	1	0.095
9	10	340	1	0.11
8	9	519	1	0.152
7	8	843	1	0.228
6	7	1513	1	0.466
5.5	6	1183	1	0.66
5	5.5	1724	1	0.58
4	5	6433	1	1.145
3.5	4	6432	1	4.267

Reflection

Resolution: 2.7→109.885 Å / Num. all: 36476 / Num. obs: 21275 / % possible obs: 93.9 % / Redundancy: 7.3 % / B_iso Wilson estimate: 108 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.156 / R_rim(I) all: 0.156 / Χ²: 1.005 / Net I/σ(I): 10.42 / Num. measured all: 287001

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.7-3	7.3	0.274	0.732	0.31	67146	11130	9056	7.328	81.4
3-3.5		0.891	1.229	1.68	82314	11151	11022	1.32	98.8
3.5-4		0.987	0.377	5.94	46216	6296	6225	0.405	98.9
4-4.5		0.996	0.175	12.62	27580	3820	3760	0.189	98.4
4.5-5		0.999	0.087	20.28	17586	2464	2423	0.093	98.3
5-6		0.999	0.073	23.67	19862	2805	2785	0.079	99.3
6-7		0.999	0.056	30.39	9886	1440	1438	0.06	99.9
7-8		0.999	0.033	45.76	5773	821	817	0.036	99.5
8-9		1	0.025	60.41	3466	502	502	0.027	100
9-10		1	0.02	69.13	2190	322	320	0.022	99.4
10-15		1	0.02	69.16	4051	628	620	0.022	98.7
15-20		1	0.019	68.41	880	155	146	0.021	94.2
20-20.944		0.999	0.022	66.29	51	128	9	0.025	7

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Phasing

Phasing

Method:

MIRAS

Phasing set

ID
1
2
3
4
5

Phasing MIR

Resolution: 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

ID	Der set-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1	0	0	16686	2008
ISO_2	2	1.14	0.903	11889	1590
ISO_3	3	2.332	2.088	6228	1031
ISO_4	4	1.191	1.37	11034	1543
ISO_5	5	0.726	0.608	12130	1612

Phasing MIR der shell

Highest resolution (Å)	Lowest resolution (Å)	Der-ID	Power acentric	Power centric	Reflection acentric	Reflection centric
12.66	20.96	ISO_1	0	0	264	104
9.9	12.66	ISO_1	0	0	390	106
8.4	9.9	ISO_1	0	0	480	105
7.42	8.4	ISO_1	0	0	577	97
6.72	7.42	ISO_1	0	0	634	110
6.19	6.72	ISO_1	0	0	704	105
5.77	6.19	ISO_1	0	0	761	100
5.42	5.77	ISO_1	0	0	808	108
5.13	5.42	ISO_1	0	0	875	105
4.88	5.13	ISO_1	0	0	900	101
4.67	4.88	ISO_1	0	0	959	108
4.48	4.67	ISO_1	0	0	1007	93
4.31	4.48	ISO_1	0	0	1044	115
4.16	4.31	ISO_1	0	0	1075	103
4.02	4.16	ISO_1	0	0	1123	98
3.9	4.02	ISO_1	0	0	900	93
3.79	3.9	ISO_1	0	0	1192	104
3.68	3.79	ISO_1	0	0	855	67
3.59	3.68	ISO_1	0	0	841	77
3.5	3.59	ISO_1	0	0	1297	109
12.66	20.96	ISO_2	1.701	1.333	263	104
9.9	12.66	ISO_2	1.29	0.696	390	106
8.4	9.9	ISO_2	1.214	0.817	480	105
7.42	8.4	ISO_2	1.241	0.961	577	97
6.72	7.42	ISO_2	1.269	0.897	634	110
6.19	6.72	ISO_2	1.065	0.827	704	105
5.77	6.19	ISO_2	0.877	0.585	761	100
5.42	5.77	ISO_2	0.628	0.569	808	108
5.13	5.42	ISO_2	0.474	0.395	873	105
4.88	5.13	ISO_2	0.342	0.324	897	101
4.67	4.88	ISO_2	0.234	0.183	958	108
4.48	4.67	ISO_2	0.158	0.149	1005	93
4.31	4.48	ISO_2	0.103	0.08	1043	115
4.16	4.31	ISO_2	0.046	0.039	1072	103
4.02	4.16	ISO_2	0.018	0.015	1120	98
3.9	4.02	ISO_2	0.049	0.041	304	32
3.79	3.9	ISO_2	0	0	0	0
3.68	3.79	ISO_2	0	0	0	0
3.59	3.68	ISO_2	0	0	0	0
3.5	3.59	ISO_2	0	0	0	0
12.66	20.96	ISO_3	4.971	3.33	259	101
9.9	12.66	ISO_3	3.23	1.93	390	106
8.4	9.9	ISO_3	2.78	1.944	479	105
7.42	8.4	ISO_3	2.481	2.109	577	97
6.72	7.42	ISO_3	2.024	1.824	634	110
6.19	6.72	ISO_3	1.542	1.175	704	105
5.77	6.19	ISO_3	1.163	0.974	759	100
5.42	5.77	ISO_3	0.707	0.673	796	107
5.13	5.42	ISO_3	0.379	0.296	859	104
4.88	5.13	ISO_3	0.194	0.167	745	86
4.67	4.88	ISO_3	0.086	0.167	26	10
4.48	4.67	ISO_3	0	0	0	0
4.31	4.48	ISO_3	0	0	0	0
4.16	4.31	ISO_3	0	0	0	0
4.02	4.16	ISO_3	0	0	0	0
3.9	4.02	ISO_3	0	0	0	0
3.79	3.9	ISO_3	0	0	0	0
3.68	3.79	ISO_3	0	0	0	0
3.59	3.68	ISO_3	0	0	0	0
3.5	3.59	ISO_3	0	0	0	0
12.66	20.96	ISO_4	4.173	2.497	261	102
9.9	12.66	ISO_4	3.507	2.455	390	106
8.4	9.9	ISO_4	2.972	2.05	480	104
7.42	8.4	ISO_4	2.177	1.599	577	97
6.72	7.42	ISO_4	1.625	1.147	633	110
6.19	6.72	ISO_4	1.078	0.929	700	105
5.77	6.19	ISO_4	0.674	0.573	760	100
5.42	5.77	ISO_4	0.467	0.35	803	108
5.13	5.42	ISO_4	0.309	0.234	869	105
4.88	5.13	ISO_4	0.202	0.189	895	101
4.67	4.88	ISO_4	0.09	0.062	950	108
4.48	4.67	ISO_4	0.058	0.053	907	89
4.31	4.48	ISO_4	0.015	0.016	993	111
4.16	4.31	ISO_4	0.006	0.005	939	92
4.02	4.16	ISO_4	0.003	0.002	541	69
3.9	4.02	ISO_4	0.005	0.004	336	36
3.79	3.9	ISO_4	0	0	0	0
3.68	3.79	ISO_4	0	0	0	0
3.59	3.68	ISO_4	0	0	0	0
3.5	3.59	ISO_4	0	0	0	0
12.66	20.96	ISO_5	0.911	0.761	261	103
9.9	12.66	ISO_5	0.738	0.512	390	106
8.4	9.9	ISO_5	0.754	0.587	480	105
7.42	8.4	ISO_5	0.817	0.629	577	97
6.72	7.42	ISO_5	0.964	0.633	634	110
6.19	6.72	ISO_5	0.937	0.643	704	105
5.77	6.19	ISO_5	0.973	0.69	761	100
5.42	5.77	ISO_5	0.884	0.751	808	108
5.13	5.42	ISO_5	0.812	0.663	874	105
4.88	5.13	ISO_5	0.688	0.561	899	100
4.67	4.88	ISO_5	0.542	0.478	956	108
4.48	4.67	ISO_5	0.518	0.457	1005	93
4.31	4.48	ISO_5	0.508	0.439	1042	115
4.16	4.31	ISO_5	0.467	0.414	1049	102
4.02	4.16	ISO_5	0.563	0.475	1108	98
3.9	4.02	ISO_5	0.377	0.391	574	56
3.79	3.9	ISO_5	0.24	0.383	8	1
3.68	3.79	ISO_5	0	0	0	0
3.59	3.68	ISO_5	0	0	0	0
3.5	3.59	ISO_5	0	0	0	0

Phasing MIR shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
12.66-20.96	0.956	0.902	264	104
9.9-12.66	0.906	0.742	390	107
8.4-9.9	0.844	0.705	480	105
7.42-8.4	0.754	0.614	577	100
6.72-7.42	0.586	0.55	639	111
6.19-6.72	0.458	0.462	704	106
5.77-6.19	0.359	0.368	763	101
5.42-5.77	0.299	0.244	814	112
5.13-5.42	0.24	0.219	877	105
4.88-5.13	0.208	0.201	930	106
4.67-4.88	0.178	0.225	972	109
4.48-4.67	0.153	0.155	1021	99
4.31-4.48	0.125	0.164	1062	119
4.16-4.31	0.118	0.094	1093	104
4.02-4.16	0.103	0.069	1132	101
3.9-4.02	0.089	0.057	965	102
3.79-3.9	0.001	0.001	1192	104
3.68-3.79	0	0	855	67
3.59-3.68	0	0	841	77
3.5-3.59	0	0	1297	109

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Processing

Software

Name	Classification
PHENIX	refinement
SHARP	phasing
DM	phasing
XDS	data reduction
XSCALE	data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.3394	1052	4.95 %
R_work	0.297	20218	-
obs	0.299	21270	61.27 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 368.39 Å² / B_iso mean: 110.3123 Å² / B_iso min: 16.96 Å²

Refinement step

Cycle: final / Resolution: 2.872→38.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5282	0	63	57	5402
B_iso mean	-	-	123.16	75.8	-
Num. residues	-	-	-	-	649

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5472
X-RAY DIFFRACTION	f_angle_d	0.744	7432
X-RAY DIFFRACTION	f_chiral_restr	0.04	842
X-RAY DIFFRACTION	f_plane_restr	0.004	914
X-RAY DIFFRACTION	f_dihedral_angle_d	17.699	3156

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.8723-3.003	0.8009	8	0.6498	204	212	5
3.003-3.1612	0.5912	27	0.5265	599	626	15
3.1612-3.3592	0.3716	55	0.4034	1251	1306	31
3.3592-3.6184	0.3957	127	0.3524	2369	2496	58
3.6184-3.9821	0.364	182	0.3043	3399	3581	83
3.9821-4.5576	0.3414	214	0.271	4058	4272	99
4.5576-5.7391	0.3043	216	0.2813	4111	4327	99
5.7391-38.706	0.3215	223	0.2877	4227	4450	98

Refinement TLS params.

Method: refined / Origin x: -25.0661 Å / Origin y: -12.366 Å / Origin z: 15.5844 Å

	11	12	13	21	22	23	31	32	33
T	0.185 Å²	-0.1934 Å²	-0.246 Å²	-	0.0821 Å²	-0.4493 Å²	-	-	-0.0025 Å²
L	2.0249 °²	0.0265 °²	0.59 °²	-	0.774 °²	-0.2781 °²	-	-	0.7621 °²
S	0.4383 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

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	all	A	30 - 810
2	X-RAY DIFFRACTION	1	all	B	3 - 80
3	X-RAY DIFFRACTION	1	all	C	1
4	X-RAY DIFFRACTION	1	all	D	1

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
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