PDB-5ufr: Structure of RORgt bound to

ID or keywords:

Entry

Database: PDB / ID: 5ufr

Title

Structure of RORgt bound to

Components

Nuclear receptor ROR-gamma

Keywords

NUCLEAR PROTEIN / Nuclear Hormone Receptor

Function / homology

Function and homology information

cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.068 Å

Authors

Spurlino, J. / Abad, M.

Citation

Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Identification and structure activity relationships of quinoline tertiary alcohol modulators of ROR gamma t.
Authors: Kummer, D.A. / Cummings, M.D. / Abad, M. / Barbay, J. / Castro, G. / Wolin, R. / Kreutter, K.D. / Maharoof, U. / Milligan, C. / Nishimura, R. / Pierce, J. / Schalk-Hihi, C. / Spurlino, J. / ...

History

Deposition	Jan 5, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 5, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 26, 2017	Group: Database references
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ufr.cif.gz	201 KB	Display	PDBx/mmCIF format
PDB format	pdb5ufr.ent.gz	163.2 KB	Display	PDB format
PDBx/mmJSON format	5ufr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ufr_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ufr_full_validation.pdf.gz	1.1 MB	Display
Data in XML	5ufr_validation.xml.gz	19.3 KB	Display
Data in CIF	5ufr_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uf/5ufr ftp://data.pdbj.org/pub/pdb/validation_reports/uf/5ufr	HTTPS FTP

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Related structure data

Related structure data	5ufoC 5uhiC C: citing same article (ref.)
Similar structure data	5k3n-4 6vsw-1 6cn6-d 4qm0-1 5ufo-d 6b31-2 5ntq-2 6cn5-2 5k3l-1 6q6m-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

Deposited unit

A: Nuclear receptor ROR-gamma

B: Nuclear receptor ROR-gamma

hetero molecules

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

1

A: Nuclear receptor ROR-gamma

hetero molecules

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

2

B: Nuclear receptor ROR-gamma

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.089, 107.053, 124.122
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma Mass: 30102.688 Da / Num. of mol.: 2 / Fragment: UNP residues 265-507 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449
#2: Chemical	ChemComp-88J / (S)-[4-chloro-2-(dimethylamino)-3-phenylquinolin-6-yl](1-methyl-1H-imidazol-5-yl)(pyridin-4-yl)methanol Mass: 469.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₂₄ClN₅O
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.87 Å³/Da / Density % sol: 57.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 1.4M NaAcetate, 100mM MES pH 6.5

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 42514 / % possible obs: 99.69 % / Redundancy: 6.1 % / Net I/σ(I): 27.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 2.068→47.717 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.93

	R_factor	Num. reflection	% reflection
R_free	0.2535	2154	5.07 %
R_work	0.2173	-	-
obs	0.2192	42514	99.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.068→47.717 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3644	0	68	1	3713

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3790
X-RAY DIFFRACTION	f_angle_d	0.76	5104
X-RAY DIFFRACTION	f_dihedral_angle_d	22.292	2264
X-RAY DIFFRACTION	f_chiral_restr	0.041	550
X-RAY DIFFRACTION	f_plane_restr	0.003	672

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 (%)
2.0677-2.1158	0.4242	118	0.3759	2656	X-RAY DIFFRACTION	100
2.1158-2.1687	0.4063	175	0.3401	2625	X-RAY DIFFRACTION	100
2.1687-2.2273	0.4143	139	0.3229	2667	X-RAY DIFFRACTION	100
2.2273-2.2929	0.3426	120	0.3017	2682	X-RAY DIFFRACTION	100
2.2929-2.3669	0.353	134	0.2846	2673	X-RAY DIFFRACTION	100
2.3669-2.4515	0.337	154	0.264	2650	X-RAY DIFFRACTION	100
2.4515-2.5496	0.2882	121	0.2518	2708	X-RAY DIFFRACTION	100
2.5496-2.6657	0.2684	143	0.2441	2681	X-RAY DIFFRACTION	100
2.6657-2.8062	0.2799	138	0.2446	2655	X-RAY DIFFRACTION	100
2.8062-2.982	0.3023	157	0.2628	2701	X-RAY DIFFRACTION	100
2.982-3.2122	0.2851	129	0.2655	2696	X-RAY DIFFRACTION	100
3.2122-3.5353	0.3189	148	0.2446	2713	X-RAY DIFFRACTION	100
3.5353-4.0467	0.2319	147	0.1944	2702	X-RAY DIFFRACTION	100
4.0467-5.0975	0.2024	149	0.1626	2735	X-RAY DIFFRACTION	99
5.0975-47.7298	0.1863	182	0.1675	2816	X-RAY DIFFRACTION	100

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	3.7517	-2.7688	5.5281	5.7373	-2.0525	9.4426	-0.0586	-1.148	1.2749	0.4534	-0.3499	-0.6723	-0.6384	-0.0332	0.5024	0.6796	-0.0737	0.0813	0.8929	-0.089	0.7349	38.7183	28.267	-4.3617
2	9.8597	2.321	-3.6032	1.4129	-1.6086	6.1	0.345	-0.6495	1.4752	-0.0666	0.069	0.5698	-1.0407	-0.6931	0.2035	0.7009	0.0743	0.0215	0.988	-0.0845	0.7415	15.619	27.8795	-7.3593
3	3.7215	-0.9012	0.3794	4.3681	3.4323	2.9784	-0.5164	-0.208	-0.0127	0.3678	-0.4997	0.7509	0.4752	-1.4549	0.6743	0.57	-0.0002	0.0103	0.9413	-0.0631	0.7141	2.0768	18.5785	-19.8578
4	7.7365	1.9498	3.0805	2.8566	2.0026	3.7043	-0.4846	0.0453	0.7231	-0.293	0.1583	0.2255	-0.2621	-0.262	0.2592	0.5353	0.0077	0.0153	0.5593	0.0595	0.5483	22.3185	22.7568	-23.7713
5	9.3701	-0.1603	-2.7828	1.3666	-1.3486	3.0033	-0.1084	-0.6168	0.2977	-0.0509	0.0565	0.1208	0.0071	0.0407	0.054	0.5368	-0.0034	-0.0184	0.572	-0.076	0.5162	35.175	20.5401	-17.9875
6	4.9581	1.5173	0.7652	2.7428	0.0348	8.0705	0.0946	-0.7669	-0.0955	0.2838	0.0013	0.3489	0.3288	-0.9773	-0.09	0.4863	-0.0632	0.0189	0.8827	0.0036	0.6137	10.3927	15.8035	-14.2721
7	7.0571	1.9314	3.2722	2.5447	-0.2716	2.1607	0.3627	-1.4732	-0.6514	0.3869	-0.3828	0.1716	1.2991	-0.5002	-0.1916	0.7443	-0.0794	-0.0199	0.7942	0.1001	0.6668	18.6276	9.4083	-11.2041
8	5.6576	-1.3266	-2.6679	2.8352	1.8377	5.1253	0.1385	-0.1107	-0.0713	0.0767	-0.2503	0.0584	0.148	-0.4452	0.1214	0.5928	0.0209	-0.0066	0.6496	0.016	0.505	35.9618	17.0859	-11.1149
9	4.8652	-0.329	-4.7903	2.1724	0.7745	4.8467	-0.1114	-1.6226	-0.1563	0.2627	0.0081	-0.0359	0.5335	0.7346	0.2151	0.6486	0.0227	-0.0041	1.0261	0.039	0.6089	43.4589	17.6134	-5.0651
10	6.5354	0.7533	2.529	3.5224	-0.9704	8.04	0.2632	-0.895	-1.2286	0.0097	0.0293	-0.2788	0.9346	0.359	-0.3202	0.7977	0.0793	-0.0046	0.6615	0.113	0.8536	30.6314	10.0554	-4.2087
11	2.1097	-2.4319	2.1427	3.9235	-3.7085	3.7928	-0.0681	-0.8655	-0.7579	0.4473	0.9031	0.091	0.2231	0.4049	-0.5992	0.7694	-0.0126	0.0505	0.904	-0.0462	0.7597	23.0519	13.5928	-29.8424
12	2.2447	1.3653	-1.3718	4.1954	-4.0816	4.0109	-0.5893	1.0623	-0.6491	-1.3638	-0.3284	-2.0434	-0.2759	1.8714	0.8261	1.1834	-0.2308	0.3136	1.3137	0.044	1.1153	37.5894	40.2563	3.0234
13	1.8722	1.097	-0.3235	3.4817	-0.2503	2.0403	0.0911	0.1424	-0.2861	-0.1674	-0.3114	-0.0151	-0.0163	-0.0386	0.3103	0.6193	-0.0687	0.0508	0.8462	-0.1225	0.5594	17.3127	24.6284	6.839
14	7.7775	0.5041	1.6286	3.8596	3.7324	3.9537	0.2502	0.636	-0.9227	0.3902	-0.3234	0.1609	1.8783	-1.9799	-0.0891	0.6827	-0.1239	0.021	0.7757	-0.088	0.6442	3.5131	20.7615	21.2923
15	3.888	2.3149	-5.1594	5.1391	-1.9479	7.1237	-0.1463	-0.3497	-1.0972	0.0242	-0.2144	-0.4199	0.3197	0.5888	0.2313	0.4809	-0.0237	-0.0479	0.4577	0.0378	0.5117	22.1866	29.7907	23.4708
16	5.6294	2.1277	3.7568	4.1163	1.3754	5.5906	-0.5059	0.2463	-0.0444	-0.3681	0.291	-0.2629	-0.5458	-0.0419	0.2419	0.5548	-0.0758	0.047	0.4816	0.0263	0.5463	31.1482	40.8226	18.3808
17	4.4332	1.4852	0.3843	2.3144	-0.1733	1.6357	-0.2577	0.3889	0.2142	-0.2471	0.0615	-0.1105	-0.3147	-0.1001	0.1464	0.6228	-0.0443	-0.0028	0.498	0.0322	0.547	16.5261	37.9828	13.4601
18	5.9029	1.1031	5.3824	2.0557	1.6831	9.2536	-1.1128	1.8233	0.672	-1.687	0.9751	-0.4278	-1.8847	0.9018	0.301	1.3073	-0.397	0.0085	0.9448	0.174	0.7638	34.515	50.6949	6.896
19	2.3876	1.1392	-2.5004	0.8991	-2.2758	5.8645	0.4406	0.6967	0.9964	-0.5027	0.298	0.0761	-2.0271	-0.4471	-0.4989	1.3149	0.0521	0.0597	0.6021	0.0658	0.7593	19.4824	48.3718	7.1898
20	2.9442	0.0132	1.4673	2.2342	-4.1488	8.4606	0.136	0.6757	0.4269	-0.3957	-0.4074	0.0731	-0.6092	0.0691	0.1524	0.6599	-0.0972	0.019	0.6577	-0.0893	0.7097	18.2054	35.9244	30.7001

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 265 through 284 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 285 through 297 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 298 through 312 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 313 through 337 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 338 through 368 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 369 through 393 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 394 through 410 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 411 through 435 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 436 through 456 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 457 through 475 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 476 through 487 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 265 through 283 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 284 through 301 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 302 through 312 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 313 through 336 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 337 through 368 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 369 through 435 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 436 through 456 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 457 through 475 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 476 through 487 )

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