PDB-5tod: Transmembrane protein 24 SMP domain

ID or keywords:

Entry

Database: PDB / ID: 5tod

Title

Transmembrane protein 24 SMP domain

Components

Transmembrane protein 24

Keywords

LIPID TRANSPORT / lipid transfer protein / SMP / membrane contact sites

Function / homology

Function and homology information

endoplasmic reticulum-plasma membrane contact site / phosphatidylinositol transfer activity / cortical endoplasmic reticulum / insulin binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phosphatidylinositol binding / membrane => GO:0016020 / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.96 Å

Authors

Lees, J.A. / Reinisch, K.M.

Funding support

United States, 1items

Citation

Journal: Science / Year: 2017
Title: Lipid transport by TMEM24 at ER-plasma membrane contacts regulates pulsatile insulin secretion.
Authors: Lees, J.A. / Messa, M. / Sun, E.W. / Wheeler, H. / Torta, F. / Wenk, M.R. / De Camilli, P. / Reinisch, K.M.

History

Deposition	Oct 17, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 8, 2017	Group: Derived calculations
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tod.cif.gz	500.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5tod.ent.gz	441.2 KB	Display	PDB format
PDBx/mmJSON format	5tod.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tod_validation.pdf.gz	468.6 KB	Display	wwPDB validaton report
Full document	5tod_full_validation.pdf.gz	472.7 KB	Display
Data in XML	5tod_validation.xml.gz	29.7 KB	Display
Data in CIF	5tod_validation.cif.gz	40.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/to/5tod ftp://data.pdbj.org/pub/pdb/validation_reports/to/5tod	HTTPS FTP

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Related structure data

Similar structure data	3md1-d 5ii9-1 6nek-d 5r4y-d 3sl9-4 7jjv-d 6tgt-d 2mbm-d 5y3s-1 5qxx-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) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

F: Transmembrane protein 24

A: Transmembrane protein 24

B: Transmembrane protein 24

C: Transmembrane protein 24

D: Transmembrane protein 24

E: Transmembrane protein 24

126 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

F: Transmembrane protein 24

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

2

A: Transmembrane protein 24

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

3

B: Transmembrane protein 24

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

4

C: Transmembrane protein 24

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

5

D: Transmembrane protein 24

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

6

E: Transmembrane protein 24

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

7

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	83.395, 117.098, 148.133
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Transmembrane protein 24 / C2 domain-containing protein 2-like Mass: 21059.260 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C2CD2L, KIAA0285, TMEM24, DLNB23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14523

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.86 Å³/Da / Density % sol: 57.02 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100-200 mM MgCl2, 100 mM bis-tris propane pH 6.5-8.0, 45% PEG 200 PH range: 6.5-8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2014
Radiation	Monochromator: Cryogenically cooled single-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.958→148.13 Å / Num. obs: 30469 / % possible obs: 98.1 % / Redundancy: 12.7 % / R_merge(I) obs: 0.093 / Net I/σ(I): 28.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.96→58.55 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.07

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.264	1942	6.5 %	THIN SHELL
R_work	0.239	-	-	-
obs	0.241	29860	96.5 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.96→58.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6900	0	0	0	6900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7031
X-RAY DIFFRACTION	f_angle_d	0.504	9605
X-RAY DIFFRACTION	f_dihedral_angle_d	11.444	4318
X-RAY DIFFRACTION	f_chiral_restr	0.043	1174
X-RAY DIFFRACTION	f_plane_restr	0.003	1229

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.9596-3.0336	0.3996	92	0.3809	1378	X-RAY DIFFRACTION	68
3.0336-3.1156	0.3628	111	0.3458	1893	X-RAY DIFFRACTION	92
3.1156-3.2073	0.3818	172	0.311	1933	X-RAY DIFFRACTION	97
3.2073-3.3108	0.339	94	0.2779	2022	X-RAY DIFFRACTION	98
3.3108-3.4291	0.3418	192	0.2692	1974	X-RAY DIFFRACTION	99
3.4291-3.5664	0.3056	98	0.2604	2065	X-RAY DIFFRACTION	99
3.5664-3.7287	0.2625	195	0.2394	1965	X-RAY DIFFRACTION	99
3.7287-3.9252	0.2571	99	0.2396	2111	X-RAY DIFFRACTION	100
3.9252-4.1711	0.2828	197	0.2305	2007	X-RAY DIFFRACTION	100
4.1711-4.493	0.2235	99	0.1991	2111	X-RAY DIFFRACTION	100
4.493-4.945	0.1965	137	0.1689	2073	X-RAY DIFFRACTION	100
4.945-5.66	0.225	160	0.2189	2062	X-RAY DIFFRACTION	100
5.66-7.129	0.2879	99	0.2595	2165	X-RAY DIFFRACTION	100
7.129-58.5604	0.2373	197	0.2477	2159	X-RAY DIFFRACTION	99

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	0.9443	0.491	-0.0591	0.2556	-0.092	1.537	0.1326	0.3429	0.2707	0.2768	0.179	-0.3834	0.0241	-0.2033	0.0008	0.6938	0.0017	0.1143	0.9245	0.0079	0.7202	48.9814	72.6408	109.5498
2	1.4738	2.1171	-0.4544	4.746	-2.2438	1.8647	0.6398	0.8343	-0.7537	-0.3682	-1.0254	-1.0735	-1.0261	-0.5365	-0.2789	1.1079	0.1202	0.0535	0.7687	-0.134	1.0163	48.7837	70.0082	119.4213
3	2.0101	-0.2123	-0.9988	2.7933	-0.5671	2.0403	0.0799	0.2871	-0.0476	-0.3701	-0.1397	0.5889	-0.0444	-0.9686	-0.0002	0.4438	0.1086	-0.025	0.9353	0.1049	0.802	42.2018	74.227	110.5475
4	1.0153	-0.6876	-0.6011	0.4997	0.1673	0.8002	-0.0051	-0.368	-0.0173	0.7684	0.1635	-0.1846	0.1134	0.0233	0.0004	0.5752	0.1349	-0.1229	0.7265	-0.0269	0.4956	62.6299	77.3512	85.3675
5	1.5311	0.6434	0.0977	2.7756	-0.3244	2.7426	-0.2904	-0.3284	0.1264	-0.0576	0.3244	0.3754	-0.3739	-0.3073	-0.0005	0.494	0.0636	-0.0344	0.5571	-0.0042	0.578	58.9608	79.2958	78.9093
6	0.6379	-1.1497	-0.3568	1.5959	1.2526	1.5235	0.016	-0.2222	-0.233	-0.0074	-0.0567	0.2979	-0.0592	-0.1348	-0.0009	0.5152	0.0189	-0.1126	0.4891	0.0132	0.4523	62.5156	68.8515	76.9962
7	0.8442	-1.0315	-0.5036	1.7153	0.4226	1.023	0.1719	0.3709	0.3739	0.6663	0.0683	0.3022	0.1445	-0.1264	0.0016	0.662	0.0071	0.0793	0.5489	0.1106	0.6435	77.5944	58.4683	92.2848
8	0.7826	0.2193	-0.7866	0.3407	-0.0284	1.3146	0.3419	0.0072	0.1256	0.2283	-0.1012	-0.1447	0.3182	-0.005	0.0007	0.6223	-0.0458	0.0002	0.5747	0.0087	0.5895	84.724	59.8389	87.1961
9	0.9978	0.8718	0.9188	0.6952	0.3863	1.8436	-0.2345	0.5476	-0.6943	-0.0702	0.1733	-0.2624	1.0682	-1.3835	-0.0262	0.6198	0.0566	-0.035	0.5574	0.0505	0.6077	77.1734	43.9874	93.1013
10	1.8749	1.8082	0.3002	3.0174	0.0102	0.6532	-0.0131	-0.1277	-0.1421	-0.0154	0.1371	-0.2664	0.0425	0.0853	0.0004	0.4886	0.0676	-0.0018	0.485	0.0201	0.5391	89.4179	59.51	91.3494
11	1.5875	-1.1364	0.062	0.7581	-0.1197	1.008	0.0517	1.1429	0.5034	-0.7656	0.3126	-1.0526	-0.612	0.6623	-0.0151	0.6545	0.1033	0.2653	0.8756	0.0733	0.754	67.3956	59.5092	118.1222
12	1.0427	-0.2477	-0.6832	0.2342	-0.3226	1.2451	0.026	0.4354	0.5003	0.3296	0.1425	0.2502	0.1253	0.1108	0.0012	0.6341	0.0725	0.1702	0.5243	0.0635	0.6217	65.711	60.5957	126.2952
13	0.7597	0.7966	0.5783	1.0188	0.7259	0.5201	0.4927	-0.7821	0.1913	0.1598	0.4106	-0.481	-0.9014	1.0861	0.0069	0.665	0.063	0.1398	0.6074	-0.0337	0.6248	82.1943	54.4339	124.0119
14	0.604	-0.315	-1.0215	2.2828	-0.0297	1.6465	-0.0676	0.2366	-0.2458	-0.1807	-0.0734	0.3311	0.4164	-0.1931	-0.001	0.6461	0.0413	0.1298	0.5577	0.0264	0.5659	62.5616	54.5906	122.3292
15	1.6296	1.2673	0.5922	1.6027	1.4054	2.045	-0.0162	0.124	-0.2015	0.3185	-0.0802	0.0048	0.3639	0.0002	-0.0038	0.4916	-0.0537	0.0853	0.5223	-0.044	0.4818	82.2712	85.0375	95.0258
16	2.2908	-0.0738	0.0422	0.0553	-0.1428	0.1417	-0.5479	0.0698	-1.8576	-0.8678	0.3156	-0.0617	-0.4843	0.0877	-0.001	0.9469	0.0284	0.0712	0.5293	-0.0144	0.6712	86.0907	79.6798	86.6853
17	1.1722	-1.0971	0.6963	1.2787	-0.3366	0.7154	-0.1467	-0.3137	0.0565	0.4914	0.3783	-0.8402	0.4864	0.3135	0.0004	0.5593	-0.0488	0.0371	0.5722	-0.1275	0.6805	95.9078	88.9152	103.1641
18	1.1608	0.0215	0.5185	2.4371	0.645	1.3067	0.0249	0.051	0.2378	-0.1839	0.0102	0.0016	-0.0925	0.132	0.0002	0.4201	-0.0759	0.0684	0.4382	-0.0139	0.5043	82.5691	90.6334	89.4358
19	1.0281	0.0466	-1.0901	1.6384	0.3141	1.2095	0.0146	0.6431	-0.1175	-1.2669	-0.3596	0.5585	-0.2208	-0.1309	-0.0048	0.8681	-0.0225	0.067	0.5965	-0.026	0.7914	66.0382	86.557	117.9158
20	0.942	-0.3205	-0.5688	0.5281	-0.461	0.8343	0.6952	0.2065	0.0936	-0.6127	-0.4693	-0.3715	0.2502	-0.2533	0.0001	0.7352	0.1436	0.0519	0.6658	0.0501	0.6884	63.9793	85.804	126.2184
21	1.1312	-0.7658	0.2585	0.6209	-0.4334	0.1753	0.0742	0.9791	0.6363	0.759	0.5369	-0.1346	-0.7686	-1.1274	0.0022	0.7898	0.0626	0.2359	0.6731	0.0481	0.8224	66.7288	100.8177	116.7098
22	1.0291	0.9243	-0.0679	2.4344	0.1331	0.229	0.0975	-0.1392	-0.056	0.7647	0.0029	-0.0149	-0.3882	0.0603	0.0003	0.5761	-0.0015	0.1032	0.5035	-0.0203	0.5796	70.5385	85.1954	127.5693

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'F' and (resid 90 through 125 )
2	X-RAY DIFFRACTION	2	chain 'F' and (resid 126 through 134 )
3	X-RAY DIFFRACTION	3	chain 'F' and (resid 135 through 256 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 89 through 114 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 115 through 160 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 161 through 255 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 89 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 140 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 141 through 160 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 161 through 255 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 97 through 114 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 115 through 140 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 141 through 160 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 161 through 256 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 89 through 125 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 126 through 134 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 135 through 160 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 161 through 256 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 89 through 114 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 115 through 140 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 141 through 160 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 161 through 256 )

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