PDB-8xu5: The Crystal Structure of RORgT from Biortus.

ID or keywords:

Entry

Database: PDB / ID: 8xu5

Title

The Crystal Structure of RORgT from Biortus.

Components

Nuclear receptor ROR-gamma

Keywords

TRANSCRIPTION / Activator / Biological rhythms / Metal-binding

Function / homology

Function and homology information

T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 /

MOLECULAR REPLACEMENT / Resolution: 3.5 Å

Authors

Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Wu, B.

Funding support

1items

Citation

Journal: To Be Published
Title: The Crystal Structure of RORgT from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Qi, J. / Wu, B.

History

Deposition	Jan 12, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xu5.cif.gz	108 KB	Display	PDBx/mmCIF format
PDB format	pdb8xu5.ent.gz	79.9 KB	Display	PDB format
PDBx/mmJSON format	8xu5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8xu5_validation.pdf.gz	423.4 KB	Display	wwPDB validaton report
Full document	8xu5_full_validation.pdf.gz	424.4 KB	Display
Data in XML	8xu5_validation.xml.gz	16.8 KB	Display
Data in CIF	8xu5_validation.cif.gz	22.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xu/8xu5 ftp://data.pdbj.org/pub/pdb/validation_reports/xu/8xu5	HTTPS FTP

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Related structure data

Similar structure data	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

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

1

A: Nuclear receptor ROR-gamma

defined by author
Evidence: gel filtration
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Nuclear receptor ROR-gamma

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

Unit cell

Length a, b, c (Å)	99.809, 99.809, 125.490
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 265 - 486 / Label seq-ID: 1 - 222

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#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: 28307.824 Da / Num. of mol.: 2 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...

Mass: 28307.824 Da / Num. of mol.: 2
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: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.19 Å³/Da / Density % sol: 61.41 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.2M sodium formate, 3% MPD, 0.1M HEPES pH 7.4+ 0.1M Adenosine-5-triphosphate diNa salt

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2023
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→46.37 Å / Num. obs: 9025 / % possible obs: 99.9 % / Redundancy: 10.4 % / R_merge(I) obs: 0.177 / Net I/σ(I): 11.1
Reflection shell	Resolution: 3.5→3.83 Å / R_merge(I) obs: 1.076 / Num. unique obs: 2156

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.5→43.256 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.936 / SU B: 36.104 / SU ML: 0.521 / Cross valid method: FREE R-VALUE / ESU R Free: 0.587
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2493	418	4.646 %
R_work	0.2011	8579	-
all	0.203	-	-
obs	-	8997	99.922 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 103.802 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.129 Å²	0.565 Å²	0 Å²
2-	-	1.129 Å²	-0 Å²
3-	-	-	-3.663 Å²

Refinement step

Cycle: LAST / Resolution: 3.5→43.256 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3738	0	0	17	3755

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.013	3813
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3647
X-RAY DIFFRACTION	r_angle_refined_deg	1.181	1.631	5130
X-RAY DIFFRACTION	r_angle_other_deg	1.169	1.573	8366
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.319	5	456
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	22.338	21.106	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.433	15	711
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.454	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.05	0.2	475
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4281
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	943
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	764
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.163	0.2	3135
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	1874
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1960
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.086	0.2	35
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.239	0.2	83
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	5.436	10.77	1830
X-RAY DIFFRACTION	r_mcbond_other	5.437	10.767	1829
X-RAY DIFFRACTION	r_mcangle_it	8.616	16.166	2284
X-RAY DIFFRACTION	r_mcangle_other	8.614	16.169	2285
X-RAY DIFFRACTION	r_scbond_it	5.172	11.407	1983
X-RAY DIFFRACTION	r_scbond_other	5.171	11.409	1984
X-RAY DIFFRACTION	r_scangle_it	8.762	16.888	2846
X-RAY DIFFRACTION	r_scangle_other	8.76	16.89	2847
X-RAY DIFFRACTION	r_lrange_it	14.686	205.048	15473
X-RAY DIFFRACTION	r_lrange_other	14.686	205.038	15473
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.106	0.05	7095

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.10613	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.10613	0.05008

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 (%)
3.5-3.591	0.401	33	0.31	635	X-RAY DIFFRACTION	100
3.591-3.689	0.311	33	0.302	619	X-RAY DIFFRACTION	100
3.689-3.796	0.323	12	0.273	609	X-RAY DIFFRACTION	100
3.796-3.913	0.382	33	0.268	581	X-RAY DIFFRACTION	100
3.913-4.041	0.249	21	0.238	554	X-RAY DIFFRACTION	100
4.041-4.182	0.269	23	0.222	558	X-RAY DIFFRACTION	100
4.182-4.34	0.205	32	0.213	529	X-RAY DIFFRACTION	100
4.34-4.516	0.304	23	0.193	484	X-RAY DIFFRACTION	100
4.516-4.717	0.291	29	0.186	505	X-RAY DIFFRACTION	100
4.717-4.946	0.268	28	0.182	444	X-RAY DIFFRACTION	100
4.946-5.213	0.264	16	0.18	458	X-RAY DIFFRACTION	100
5.213-5.528	0.31	24	0.186	420	X-RAY DIFFRACTION	100
5.528-5.907	0.179	21	0.201	386	X-RAY DIFFRACTION	100
5.907-6.378	0.226	18	0.221	365	X-RAY DIFFRACTION	100
6.378-6.983	0.477	20	0.205	334	X-RAY DIFFRACTION	100
6.983-7.801	0.356	7	0.194	319	X-RAY DIFFRACTION	100
7.801-8.996	0.182	18	0.146	269	X-RAY DIFFRACTION	100
8.996-10.988	0.105	16	0.113	223	X-RAY DIFFRACTION	100
10.988-15.415	0.19	9	0.15	182	X-RAY DIFFRACTION	100
15.415-43.256	0.177	2	0.228	105	X-RAY DIFFRACTION	93.8596

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