PDB-2fim: Structure of the C-terminal domain of Human Tubby-like protein 1

ID or keywords:

Entry

Database: PDB / ID: 2fim

Title

Structure of the C-terminal domain of Human Tubby-like protein 1

Components

Tubby related protein 1

Keywords

SIGNALING PROTEIN / TUBBY FILLED-BARREL / BETA-BARREL / FILLED-BETA-ROLL / 12-STRANDED-BETA-BARREL / HELIX-FILLED-BARREL / Retinitis pigmentosa / Blindness / STRUCTURAL GENOMICS

Function / homology

Function and homology information

protein localization to photoreceptor outer segment / detection of light stimulus involved in visual perception / eye photoreceptor cell development / phagocytosis, recognition / photoreceptor cell maintenance / protein localization to cilium / retina homeostasis / dendrite development / photoreceptor outer segment / axon terminus ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Hallberg, B.M. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. ...

Citation

Journal: To be published
Title: Structure of the C-terminal domain of Human Tubby-like protein 1
Authors: Persson, C. / Ogg, D. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / ...

History

Deposition	Dec 29, 2005	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 7, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2fim.cif.gz	109.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2fim.ent.gz	84.6 KB	Display	PDB format
PDBx/mmJSON format	2fim.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2fim_validation.pdf.gz	698.2 KB	Display	wwPDB validaton report
Full document	2fim_full_validation.pdf.gz	711.1 KB	Display
Data in XML	2fim_validation.xml.gz	20.3 KB	Display
Data in CIF	2fim_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fi/2fim ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fim	HTTPS FTP

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Related structure data

Similar structure data	4y93-d 3c5n-d 2xto-d 2jjd-2 1mky-d 3rmv-1 3wdw-d 4dof-2 3khc-d 5vr6-d 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

Deposited unit

A: Tubby related protein 1

B: Tubby related protein 1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	55.960, 85.150, 58.790
Angle α, β, γ (deg.)	90.00, 92.93, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Tubby related protein 1 / Tubby-like protein 1 Mass: 31446.715 Da / Num. of mol.: 2 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: O00294
#2: Chemical	ChemComp-3DP / 3-(N,N-DIMETHYLOCTYLAMMONIO)PROPANESULFONATE Mass: 279.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₃H₂₉NO₃S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.22 Å³/Da / Density % sol: 44.67 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2M AS, 25% PEG 4000, 15% glycerol, 50mM 3-(N,N-Dimethyloctylammonio)propanesulfonate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.978 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Oct 26, 2005
Radiation	Monochromator: Si-111 Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.9→40 Å / Num. all: 43277 / Num. obs: 43277 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / R_merge(I) obs: 0.061 / Net I/σ(I): 15.9
Reflection shell	Resolution: 1.9→2 Å / R_merge(I) obs: 0.239 / Mean I/σ(I) obs: 5.5 / Num. unique all: 6142 / Num. unique obs: 7645 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC		refinement
PDB_EXTRACT	1.701	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→19.89 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.941 / SU B: 7.888 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.235	2228	5.2 %	RANDOM
R_work	0.199	-	-	-
all	0.201	43243	-	-
obs	0.201	43243	99.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.966 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0.02 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3683	0	28	130	3841

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	3786
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3489
X-RAY DIFFRACTION	r_angle_refined_deg	1.8	1.966	5120
X-RAY DIFFRACTION	r_angle_other_deg	0.914	3.001	8027
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.368	5	449
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.611	22.513	191
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.827	15	640
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.688	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	557
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4168
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	833
X-RAY DIFFRACTION	r_nbd_refined	0.218	0.2	563
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	3302
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	1739
X-RAY DIFFRACTION	r_nbtor_other	0.085	0.2	2397
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.146	0.2	132
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.337	0.2	25
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.303	0.2	54
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.125	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.253	1.5	2899
X-RAY DIFFRACTION	r_mcbond_other	0.324	1.5	914
X-RAY DIFFRACTION	r_mcangle_it	1.568	2	3680
X-RAY DIFFRACTION	r_scbond_it	2.51	3	1738
X-RAY DIFFRACTION	r_scangle_it	3.596	4.5	1440

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.307	156	-
R_work	0.246	2981	-
obs	-	3137	99.56 %

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	6.0279	-0.4707	2.2695	5.9254	-1.3287	6.8762	-0.0952	-0.2656	-0.011	0.4521	0.1562	-0.1404	-0.262	-0.247	-0.0609	-0.1066	0.0892	0.013	-0.0868	-0.0008	-0.1887	85.274	2.746	30.03
2	18.0104	-11.5429	-8.6955	16.9609	7.1485	18.7294	0.1339	0.4472	-0.0337	0.7031	0.0303	0.1196	0.0498	-0.5021	-0.1642	-0.0803	-0.015	-0.0618	-0.0992	0.0843	-0.2319	86.501	-4.464	34.358
3	5.6977	0.9183	-6.235	1.5086	-3.1836	29.796	0.3679	0.3013	0.2324	0.4257	0.0689	-0.0718	-1.6123	-1.1243	-0.4368	0.1031	0.1331	-0.0653	-0.0417	0.0481	-0.1464	86.999	-6.419	33.997
4	12.5536	-1.0989	-17.4994	2.3727	2.3354	33.9549	1.2887	0.1505	0.3742	0.0052	0.1007	-0.313	-1.6895	-0.357	-1.3894	-0.0354	0.0915	0.029	-0.148	0.0154	-0.1442	89.664	-7.55	20.381
5	6.2141	6.8194	-3.2709	13.043	-5.0067	2.083	0.5331	-0.2982	0.365	0.6738	-0.356	-0.2328	0.1153	-0.0323	-0.177	-0.2238	0.0825	-0.0116	-0.1507	-0.0237	-0.1328	92.022	2.996	17.657
6	4.5148	-0.1139	2.2699	8.0831	-0.0262	3.4282	-0.0988	0.3631	0.0894	-0.0232	0.2546	-0.0859	0.1294	-0.1016	-0.1558	-0.1766	0.0046	-0.0371	-0.1212	0.0355	-0.2264	83.262	-1.922	16.342
7	7.2286	5.9741	-0.4741	22.9761	-6.5663	18.9199	0.5087	-0.5414	-0.2239	1.3959	-0.3577	-0.7072	-0.6992	0.5963	-0.151	0.0239	-0.0491	-0.0549	0.0133	-0.0373	-0.0629	83.217	-10.332	17.963
8	62.3499	41.5515	5.3901	42.427	9.336	13.8092	2.308	-3.0683	2.2598	1.9479	-1.9087	1.2769	-0.3068	0.2036	-0.3993	-0.1054	-0.0701	0.0955	-0.0519	-0.0392	-0.1416	83.945	4.271	17.043
9	3.8766	2.5459	-0.3597	6.1256	0.5464	5.2267	-0.0212	0.3364	0.2077	0.2039	0.1352	0.1721	0.366	-0.233	-0.1141	-0.1978	0.0405	0.0363	-0.1389	0.0209	-0.2029	82.643	3.208	16.22
10	4.3848	0.5498	1.3326	5.9133	-1.1738	4.706	0.0425	0.0339	0.0674	0.2008	0.2002	0.0804	0.0728	-0.1812	-0.2426	-0.183	0.0529	0.0101	-0.1601	-0.0028	-0.2363	83.452	2.24	23.309
11	3.8238	1.0449	-1.4059	5.7018	-0.3703	9.4001	0.0064	0.0973	0.0437	0.0853	-0.1422	0.3297	0.0849	-0.1258	0.1358	-0.2872	-0.0268	-0.0374	-0.1231	-0.0007	-0.0901	54.915	21.596	5.329
12	21.0643	-10.7544	8.6135	21.5919	-9.3532	12.8562	0.0345	0.6938	0.2689	-0.096	-0.6125	0.109	0.1459	0.5729	0.5779	-0.277	-0.0523	0.0349	-0.0326	-0.0719	-0.1451	52.869	16.282	5.575
13	18.0188	-0.5741	5.4621	6.775	-1.9536	5.5645	-0.5885	0.6865	0.2193	0.3498	-0.0379	0.0648	-0.1279	0.1856	0.6264	-0.2353	-0.0774	-0.0357	-0.0444	-0.0093	-0.1681	59.234	14.341	3.498
14	5.5961	2.2036	2.7123	5.6625	1.6682	6.3399	-0.3265	-0.2275	-0.3017	-0.1623	-0.038	-0.1992	-0.1429	-0.2567	0.3645	-0.2523	0.0086	0.0076	-0.1503	0.015	-0.1063	65.109	9.7	4.335
15	12.5575	4.1773	-0.9994	24.6821	4.1691	6.1807	0.1674	0.2224	0.5374	-0.4946	-0.1754	0.7201	-0.0323	0.1042	0.008	-0.0868	-0.1121	0.0283	-0.1204	-0.0255	-0.0435	58.969	-1.493	-8.285
16	5.2469	5.2226	3.3112	9.992	5.6974	9.8641	-0.0361	-0.0775	-0.2604	0.1859	-0.0668	-0.0342	0.1354	-0.3272	0.1028	-0.2341	0.0304	0.0058	-0.1775	0.0426	-0.1391	66.408	13.769	3.128
17	12.0963	3.276	12.2303	17.1515	16.6114	55.8361	-0.0428	-1.1079	0.1249	-0.3825	-0.8319	1.041	-2.4369	-4.6888	0.8747	-0.1129	0.1599	-0.0162	0.1396	0.0578	-0.0856	67.262	22.217	2.316
18	3.8769	1.3534	-0.455	7.3915	1.159	4.1328	-0.1684	0.0476	0.3415	-0.1108	0.179	0.0619	-0.5681	0.2119	-0.0106	-0.1401	-0.035	-0.0454	-0.1355	0.0686	-0.1253	67.986	28.844	0.987
19	14.7612	-3.4787	-0.6398	1.1287	-1.1733	5.7043	0.654	1.2193	-1.2574	0.6453	-0.0081	0.2749	0.5016	-0.9918	-0.646	-0.0037	0.0235	0.0484	0.1307	0.0094	0.1678	48.508	28.37	2.976
20	5.1238	1.1551	-2.44	4.4469	0.364	3.0552	-0.1084	0.1604	-0.0871	-0.0072	-0.0569	0.2144	-0.0889	-0.031	0.1654	-0.2623	0.0091	-0.0383	-0.1902	0.0047	-0.1596	60.764	22.031	1.869

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	A	A	238 - 279	25 - 66
2	2	A	A	280 - 292	67 - 79
3	3	A	A	293 - 305	80 - 92
4	4	A	A	312 - 326	99 - 113
5	5	A	A	327 - 355	114 - 142
6	6	A	A	356 - 386	143 - 173
7	7	A	A	387 - 402	174 - 189
8	8	A	A	403 - 409	190 - 196
9	9	A	A	410 - 445	197 - 232
10	10	A	A	446 - 483	233 - 270
11	11	B	B	238 - 279	25 - 66
12	12	B	B	280 - 289	67 - 76
13	13	B	B	290 - 319	77 - 106
14	14	B	B	320 - 334	107 - 121
15	15	B	B	335 - 346	122 - 133
16	16	B	B	347 - 365	134 - 152
17	17	B	B	366 - 370	153 - 157
18	18	B	B	371 - 412	158 - 199
19	19	B	B	413 - 432	200 - 219
20	20	B	B	433 - 483	220 - 270

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