PDB-5uyx: Structure of Human T-complex protein 1 subunit epsilon (CCT5)

ID or keywords:

Entry

Database: PDB / ID: 5uyx

Title

Structure of Human T-complex protein 1 subunit epsilon (CCT5)

Components

T-complex protein 1 subunit epsilon

Keywords

CHAPERONE / chaperonin Hexadecameric complex ATP-dependent CCT5 gene

Function / homology

Function and homology information

positive regulation of protein localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / : / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / beta-tubulin binding ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Pereira, J.H. / McAndrew, R.P. / Sergeeva, O.A. / Ralston, C.Y. / King, J.A. / Adams, P.D.

Citation

Journal: Sci Rep / Year: 2017
Title: Structure of the human TRiC/CCT Subunit 5 associated with hereditary sensory neuropathy.
Authors: Pereira, J.H. / McAndrew, R.P. / Sergeeva, O.A. / Ralston, C.Y. / King, J.A. / Adams, P.D.

History

Deposition	Feb 24, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 5, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uyx.cif.gz	752.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5uyx.ent.gz	633.5 KB	Display	PDB format
PDBx/mmJSON format	5uyx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uy/5uyx ftp://data.pdbj.org/pub/pdb/validation_reports/uy/5uyx	HTTPS FTP

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Related structure data

Related structure data	5uyzC 4v81S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5uyz-1 1398 3izm-d 1a6d-1 1q3s-1 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	#32 - Aug 2002 Chaperones similarity (6) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: T-complex protein 1 subunit epsilon

B: T-complex protein 1 subunit epsilon

C: T-complex protein 1 subunit epsilon

D: T-complex protein 1 subunit epsilon

hetero molecules

241 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: T-complex protein 1 subunit epsilon

B: T-complex protein 1 subunit epsilon

C: T-complex protein 1 subunit epsilon

D: T-complex protein 1 subunit epsilon

hetero molecules

A: T-complex protein 1 subunit epsilon

B: T-complex protein 1 subunit epsilon

C: T-complex protein 1 subunit epsilon

D: T-complex protein 1 subunit epsilon

hetero molecules

A: T-complex protein 1 subunit epsilon

B: T-complex protein 1 subunit epsilon

C: T-complex protein 1 subunit epsilon

D: T-complex protein 1 subunit epsilon

hetero molecules

A: T-complex protein 1 subunit epsilon

B: T-complex protein 1 subunit epsilon

C: T-complex protein 1 subunit epsilon

D: T-complex protein 1 subunit epsilon

hetero molecules

defined by author&software
Evidence: microscopy, double back to back of homo-octameric rings hexadecameric complex
963 kDa, 16 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	204.710, 204.710, 162.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

#1: Protein	T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon Mass: 59749.957 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Escherichia coli (E. coli) / References: UniProt: P48643
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.57 Å³/Da / Density % sol: 65.56 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 0.1 M Sodium acetate, 0.04 Mcitric acid, 0.06 MBis-tris propane pH 6.4, 25 %PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.5→75.7 Å / Num. obs: 44068 / % possible obs: 100 % / Redundancy: 13.3 % / Net I/σ(I): 13.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2650: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4V81

4v81

Resolution: 3.5→75.7 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.42 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3182	2215	5.03 %
R_work	0.2686	-	-
obs	0.2711	44057	99.67 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.5→75.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14641	0	108	0	14749

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14924
X-RAY DIFFRACTION	f_angle_d	0.663	20135
X-RAY DIFFRACTION	f_dihedral_angle_d	3.151	9293
X-RAY DIFFRACTION	f_chiral_restr	0.043	2381
X-RAY DIFFRACTION	f_plane_restr	0.004	2583

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 (%)
3.5-3.5761	0.4128	134	0.3628	2564	X-RAY DIFFRACTION	99
3.5761-3.6593	0.3725	129	0.3381	2558	X-RAY DIFFRACTION	100
3.6593-3.7508	0.3555	131	0.3183	2564	X-RAY DIFFRACTION	100
3.7508-3.8522	0.3916	149	0.3119	2586	X-RAY DIFFRACTION	100
3.8522-3.9656	0.3608	151	0.3047	2583	X-RAY DIFFRACTION	100
3.9656-4.0935	0.3375	132	0.2912	2577	X-RAY DIFFRACTION	100
4.0935-4.2398	0.3346	126	0.2784	2582	X-RAY DIFFRACTION	100
4.2398-4.4096	0.278	128	0.2638	2605	X-RAY DIFFRACTION	100
4.4096-4.6102	0.3328	136	0.2474	2596	X-RAY DIFFRACTION	100
4.6102-4.8533	0.3357	121	0.2487	2630	X-RAY DIFFRACTION	100
4.8533-5.1573	0.285	140	0.257	2597	X-RAY DIFFRACTION	100
5.1573-5.5554	0.3295	138	0.2896	2628	X-RAY DIFFRACTION	100
5.5554-6.1142	0.3601	141	0.3016	2641	X-RAY DIFFRACTION	100
6.1142-6.9984	0.3134	162	0.2942	2631	X-RAY DIFFRACTION	100
6.9984-8.8151	0.2905	135	0.2262	2698	X-RAY DIFFRACTION	100
8.8151-75.7174	0.2774	162	0.2347	2802	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	2.6527	0.1244	-0.3514	5.4973	1.1225	3.9134	0.0408	-0.408	-0.4356	0.0852	0.1707	-0.0552	0.3241	0.402	-0.1783	0.4477	0.0557	-0.0454	0.6295	-0.013	0.8439	63.1347	19.9407	78.6685
2	1.4006	0.688	-1.1317	0.4059	-1.9077	2.3689	0.0163	-0.3096	0.1529	0.2772	0.3989	-0.0678	-0.1097	-0.0041	-0.3701	0.924	0.1272	0.0238	0.9272	-0.1742	0.7426	46.365	17.3369	96.5735
3	1.2719	-1.084	1.5654	-0.1856	-2.0283	1.7697	0.1908	-0.1074	-0.0151	-0.1042	-0.0779	0.168	0.0133	0.045	-0.1091	1.0509	0.227	-0.0583	1.09	0.0351	0.8876	62.5203	6.9258	118.7104
4	3.6154	1.8115	-0.8562	3.0455	-0.0651	2.3367	0.1446	0.2813	-0.0557	-0.0466	0.0153	0.3789	-0.4222	-0.4322	-0.1532	0.5992	0.1826	0.0692	0.495	0.0822	0.9745	48.2289	26.9789	73.8668
5	5.5355	3.9769	-2.3754	6.0856	-1.8599	3.9276	-0.1029	-0.2341	-0.7739	-0.2773	-0.1254	-0.7925	0.399	0.24	0.2834	0.5851	0.1055	0.0263	0.4548	-0.0288	0.8627	88.3259	41.7713	78.7463
6	2.145	-0.4056	-2.333	2.3199	-0.1191	4.5332	0.4034	-0.3298	0.1754	0.6563	0.1021	0.2516	-0.1889	-0.0466	-0.5645	0.6418	0.2116	-0.164	0.5142	0.007	0.6997	76.812	56.1292	95.1372
7	0.0193	-1.5686	0.8119	1.7009	-2.3221	2.7918	-0.045	-0.3207	-0.0755	0.0065	0.3338	0.2846	-0.0455	-0.3411	-0.2252	1.2264	-0.0349	0.0005	1.0476	0.1008	1.0378	79.6452	31.1345	123.6819
8	4.1644	-0.498	-0.7341	2.4291	0.029	2.213	-0.1508	-0.0074	0.037	-0.0278	0.0417	0.0124	-0.1671	-0.2356	0.0867	0.5275	0.0077	0.024	0.4553	-0.0793	0.6748	82.6407	56.4878	77.4774
9	5.9541	-0.0421	-3.6826	2.8366	1.6592	3.3356	-0.1172	0.4435	-0.8939	-0.3566	-0.0189	-0.0727	-0.1935	-0.2988	0.0688	0.6174	-0.0102	-0.036	0.5432	0.0597	0.5469	97.1785	52.8656	40.5675
10	-0.0488	1.1322	0.6285	2.0602	3.2981	3.4416	0.1306	0.1015	0.2999	-0.9174	-0.4633	0.1201	-0.7713	-0.4432	0.1881	1.5647	0.1578	0.2137	1.3	0.0296	1.3874	106.498	42.8456	1.4262
11	2.1977	0.9826	-2.2477	5.0341	3.6439	5.392	0.9132	-0.0901	0.7599	-0.9689	-0.0548	-1.1007	-1.2392	-0.248	-0.7548	1.6618	0.0564	0.1334	1.0587	-0.0945	1.178	108.4152	44.8866	2.8701
12	5.0467	3.3996	-1.0968	3.4825	-0.4462	3.0541	0.0387	0.3895	0.7351	-0.3529	0.2171	-0.1334	-0.7849	-0.2999	-0.2134	0.6328	0.0811	0.1202	0.4597	0.0134	0.8137	98.9422	60.8289	44.2168
13	5.8535	2.1133	0.2407	7.1009	-1.9785	5.1934	0.3535	0.0723	-0.1856	0.7674	-0.4316	0.0618	-0.3257	0.7141	0.2842	0.6057	-0.0121	-0.1346	0.7628	-0.0196	0.9594	73.32	30.2198	43.1014
14	2.1042	2.2023	-3.5719	2.139	-3.8804	7.2407	-1.0314	0.752	-2.2333	-1.4106	-0.5583	-3.3742	1.8378	-0.3263	1.1413	0.8128	-0.0302	0.1499	0.7882	0.0076	1.4159	73.6647	29.0916	36.1957
15	1.6472	1.507	-3.8701	4.4408	-3.9965	6.0766	0.2224	0.3707	-0.1094	-0.6963	-0.0697	-0.4566	0.6875	-0.5174	0.0334	0.5673	0.1037	0.0171	0.719	-0.1094	0.7632	56.0653	36.4212	39.3486
16	0.8113	-0.8693	-1.88	0.7131	1.2678	2.0448	0.1984	0.0435	0.1011	0.332	0.2239	-0.0539	-0.1779	-0.5818	-0.3756	1.516	0.4017	0.1166	1.4895	0.2427	1.6768	67.6359	41.5221	7.6914
17	0.9362	0.3955	0.3001	2.5238	-1.1999	1.5993	0.1512	-0.0636	0.7383	-0.5537	0.0271	-0.0579	-0.6471	0.6672	-0.3193	1.016	0.2471	0.1818	1.3164	-0.124	0.9497	87.0931	15.805	-11.4473
18	2.313	0.9321	-0.7708	2.1571	0.203	6.5971	0.9242	1.0527	0.7751	-0.0024	0.1227	0.2755	-0.9072	-0.7485	-0.8443	1.4181	0.5257	0.0806	1.9528	0.0344	1.25	74.371	29.5441	-2.1066
19	3.9563	0.0591	-2.1727	3.5788	-1.8141	3.0818	1.5949	0.9648	0.013	-0.4228	-0.437	-1.7273	-3.2315	1.877	-1.2926	1.3518	0.1506	0.2379	1.0555	-0.3714	0.6463	70.534	44.9976	7.7783
20	1.2998	-0.9037	0.0597	7.4577	-0.8214	3.7443	0.0668	-0.1957	0.4627	-0.2895	0.2503	0.3976	-0.878	-0.6478	-0.3216	0.7532	0.1738	0.0847	0.6279	0.0969	0.8734	55.5258	42.2252	45.4233

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 31 through 129 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 130 through 241 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 242 through 414 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 415 through 536 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 31 through 129 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 130 through 230 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 231 through 393 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 394 through 536 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 31 through 182 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 183 through 295 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 296 through 397 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 398 through 536 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 31 through 67 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 68 through 91 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 92 through 183 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 184 through 256 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 257 through 293 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 294 through 356 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 357 through 405 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 406 through 528 )

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