PDB-4n5q: Crystal structure of the N-terminal ankyrin repeat domain of TRPV3

ID or keywords:

Entry

Database: PDB / ID: 4n5q

Title

Crystal structure of the N-terminal ankyrin repeat domain of TRPV3

Components

Transient receptor potential cation channel subfamily V member 3

Keywords

PROTEIN BINDING /

ankyrin / channel

Function / homology

Function and homology information

negative regulation of hair cycle /

TRP channels / response to temperature stimulus / positive regulation of calcium ion import / monoatomic cation channel activity /

calcium channel activity / monoatomic ion channel activity /

receptor complex /

membrane / identical protein binding
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.946 Å

Authors

Shi, D.J. / Ye, S. / Cao, X. / Wang, K.W. / Zhang, R.

Citation

Journal: Protein Cell / Year: 2013
Title: Crystal structure of the N-terminal ankyrin repeat domain of TRPV3 reveals unique conformation of finger 3 loop critical for channel function
Authors: Shi, D.J. / Ye, S. / Cao, X. / Zhang, R. / Wang, K.

History

Deposition	Oct 10, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jan 29, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 20, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4n5q.cif.gz	222.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4n5q.ent.gz	181.8 KB	Display	PDB format
PDBx/mmJSON format	4n5q.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/4n5q ftp://data.pdbj.org/pub/pdb/validation_reports/n5/4n5q	HTTPS FTP

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Related structure data

Similar structure data	1tq9-d 1wud-d 2etc-2 7lt8-d 2ec2-3 3fux-1 2ouw-d 2gx5-1 3bcm-d 4p78-d Search similar-shape structures by Omokage search (details) 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	#250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (3) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1)

Deposited unit

A: Transient receptor potential cation channel subfamily V member 3

B: Transient receptor potential cation channel subfamily V member 3

58.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transient receptor potential cation channel subfamily V member 3

defined by author&software
29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Transient receptor potential cation channel subfamily V member 3

defined by author&software
29.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	61.518, 78.557, 82.975
Angle α, β, γ (deg.)	90.00, 93.30, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Transient receptor potential cation channel subfamily V member 3 / TrpV3 Mass: 29344.512 Da / Num. of mol.: 2 / Fragment: UNP residues 118-367 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trpv3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K424
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 538 / 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: 3.41 Å³/Da / Density % sol: 63.94 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 2.4M sodium formate, 0.1M BIS-TRIS propane, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 2, 2013
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.946→41.4 Å / Num. all: 57774 / Num. obs: 57543 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.phaser)	model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.946→41.4 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.201	2912	5.06 %	random
R_work	0.1689	-	-	-
all	0.171	57774	-	-
obs	0.1705	57503	99.27 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.946→41.4 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4004	0	0	538	4542

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	4065
X-RAY DIFFRACTION	f_angle_d	1.575	5485
X-RAY DIFFRACTION	f_dihedral_angle_d	16.595	1547
X-RAY DIFFRACTION	f_chiral_restr	0.117	626
X-RAY DIFFRACTION	f_plane_restr	0.007	720

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.946-1.9781	0.3055	133	0.265	2405	92
1.9781-2.0122	0.3097	143	0.2456	2541	99
2.0122-2.0488	0.2957	125	0.231	2620	99
2.0488-2.0882	0.2478	147	0.209	2588	100
2.0882-2.1308	0.2211	160	0.2018	2570	100
2.1308-2.1772	0.2623	125	0.1933	2614	100
2.1772-2.2278	0.2232	147	0.1909	2586	100
2.2278-2.2835	0.223	147	0.185	2616	100
2.2835-2.3452	0.2215	116	0.1724	2598	100
2.3452-2.4143	0.2013	134	0.1698	2629	100
2.4143-2.4922	0.2004	126	0.1718	2634	100
2.4922-2.5812	0.2195	151	0.1745	2599	100
2.5812-2.6846	0.2163	146	0.181	2596	100
2.6846-2.8067	0.2147	134	0.1676	2640	100
2.8067-2.9546	0.2138	132	0.1734	2629	100
2.9546-3.1397	0.1862	145	0.1681	2592	100
3.1397-3.382	0.1729	142	0.1573	2632	100
3.382-3.7222	0.177	133	0.1439	2634	100
3.7222-4.2603	0.161	152	0.1359	2619	100
4.2603-5.3657	0.1747	136	0.1464	2641	100
5.3657-41.4279	0.2059	138	0.1822	2608	96

Refinement TLS params.

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

ID	L11 (°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)
1	4.2858	0.2511	-1.5746	1.9973	-0.574	4.0249	0.4305	-0.269	0.8025	0.1145	-0.1821	-0.3807	-0.6711	1.2689	-0.2465	0.2452	-0.0832	0.0425	0.3432	-0.107	0.4629	27.9977	91.2653	35.4106
2	4.3477	0.5116	-1.8496	1.6315	-0.7891	3.8564	0.1543	0.0055	0.3326	-0.1113	-0.0328	-0.0553	-0.0601	0.2414	-0.1241	0.1694	0.0222	0.0049	0.1938	-0.0226	0.2628	21.3119	85.7877	32.7589
3	3.6264	1.1563	-1.0056	1.7522	-0.8833	2.2026	0.0394	-0.1165	-0.4848	-0.0953	-0.0647	-0.3296	0.3016	0.2253	-0.0021	0.1714	0.0333	-0.0236	0.1701	-0.0046	0.2365	10.9297	73.8207	37.5676
4	2.9641	2.221	0.2144	5.482	-0.8334	2.4643	-0.068	-0.0269	-0.0551	-0.1516	0.0371	0.0542	-0.0874	0.0055	0.1047	0.1383	0.0051	0.0106	0.1799	0.0242	0.1863	-2.5708	71.9682	36.1461
5	1.7338	-0.114	-0.4097	2.9297	-2.0177	3.4236	0.0675	-1.3874	-0.577	1.4417	-0.3512	-0.1823	-0.1075	0.1666	0.0657	0.5431	-0.0776	-0.0115	0.5256	0.2133	0.2979	-1.5348	60.2464	49.1985
6	3.566	1.6877	-0.2416	5.7324	0.194	3.1555	-0.0163	-0.0208	0.1386	-0.14	0.0426	0.4962	-0.0499	-0.2813	0.1304	0.156	-0.0291	0.028	0.2228	0.0352	0.2938	-8.7292	64.3385	39.8522
7	5.1517	0.9818	-0.6914	4.5544	-0.8221	3.7069	0.4298	-0.4863	-0.1273	0.1817	-0.1868	0.1346	0.1754	0.1772	0.3542	0.2085	-0.0846	0.1045	0.1941	0.0588	0.3212	-9.5438	55.2527	45.3985
8	4.5151	-0.2579	0.5329	4.0631	-0.3806	5.2903	-0.2123	-0.4101	0.3365	0.2041	0.0275	-0.0397	-0.4676	0.0468	0.0828	0.2415	0.0289	-0.034	0.1499	-0.0377	0.1532	45.4098	82.0653	26.2609
9	2.6731	0.226	1.0798	7.0614	0.9229	3.6036	0.1964	0.2664	-0.1744	-0.1178	-0.1789	-1.022	-0.6366	1.1666	0.0886	0.2267	-0.0444	-0.0293	0.4115	0.0152	0.2917	57.7756	76.9938	20.0777
10	3.3188	0.5409	0.918	1.9469	0.7853	2.8115	-0.039	0.1471	-0.2785	-0.0295	0.0476	-0.0855	0.1831	0.0604	0.0233	0.1661	0.0183	0.0162	0.1432	-0.0268	0.1629	40.8798	70.011	14.9592
11	0.9542	0.9767	0.8706	3.5325	2.2312	2.7751	0.0839	0.0585	-0.1698	0.0504	0.046	-0.0301	0.1021	0.1197	-0.134	0.231	-0.0208	-0.0261	0.2607	-0.059	0.2634	33.3821	57.9224	6.0446
12	5.4189	-1.1421	1.1653	7.8871	0.9105	8.0802	-0.0973	-0.323	-0.2743	0.2588	-0.0214	0.768	-0.2995	-1.0569	-0.0037	0.2812	-0.0261	-0.0693	0.3888	-0.0669	0.3715	21.5501	54.9026	0.4211
13	3.3202	1.2311	0.3774	5.443	-0.196	3.7507	-0.1415	0.1895	-0.3368	-0.3574	0.3748	-0.4111	0.2758	0.4782	-0.2501	0.32	-0.0007	-0.0531	0.2951	-0.0673	0.2681	32.4444	45.4018	-4.0077
14	6.3572	-1.9135	4.7614	1.8997	-2.3381	6.2242	-0.4467	0.2726	0.1376	-0.2568	0.2065	0.7184	-1.0732	-0.346	0.18	0.4492	-0.0091	-0.1307	0.2228	-0.0669	0.3159	18.3559	48.5805	-10.2894

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 117 through 147 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 148 through 196 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 197 through 274 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 275 through 298 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 299 through 315 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 316 through 343 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 344 through 365 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 117 through 148 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 149 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 246 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 247 through 306 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 307 through 328 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 329 through 353 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 354 through 370 )

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