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- PDB-3b0w: Crystal structure of the orphan nuclear receptor ROR(gamma)t liga... -

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Basic information

Entry
Database: PDB / ID: 3b0w
TitleCrystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION/INHIBITOR / THREE-LAYERED ALPHA HELICAL SANDWICH / ORPHAN NUCLEAR RECEPTOR / LIGAND-BINDING DOMAIN / ANTAGONIST / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated 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 ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated 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 / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIGOXIN / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFujita-Sato, S. / Ito, S. / Isobe, T. / Ohyama, T. / Wakabayashi, K. / Morishita, K. / Ando, O. / Isono, F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis of Digoxin That Antagonizes ROR{gamma}t Receptor Activity and Suppresses Th17 Cell Differentiation and Interleukin (IL)-17 Production
Authors: Fujita-Sato, S. / Ito, S. / Isobe, T. / Ohyama, T. / Wakabayashi, K. / Morishita, K. / Ando, O. / Isono, F.
History
DepositionJun 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 28, 2011Group: Database references / Structure summary
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1784
Polymers56,6162
Non-polymers1,5622
Water1,31573
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0892
Polymers28,3081
Non-polymers7811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0892
Polymers28,3081
Non-polymers7811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.716, 98.716, 129.176
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / Retinoid-related ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / Retinoid-related orphan receptor-gamma


Mass: 28307.824 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN, UNP residues 265-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51449
#2: Chemical ChemComp-DGX / DIGOXIN


Mass: 780.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H64O14 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.2M Na formate, 3% (v/v) 2-Methyl-2,4-pentanediol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 36249 / % possible obs: 99.8 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 44.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L0L

3l0l


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.091 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 1791 5 %RANDOM
Rwork0.21176 ---
all0.21364 34265 --
obs0.21364 34265 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 110 73 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213708
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.995014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6525430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93823.073179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98515673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2121532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022694
X-RAY DIFFRACTIONr_mcbond_it0.6631.52146
X-RAY DIFFRACTIONr_mcangle_it1.31923441
X-RAY DIFFRACTIONr_scbond_it2.16131562
X-RAY DIFFRACTIONr_scangle_it3.6064.51573
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 146 -
Rwork0.238 2495 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.9365-1.1366-0.55923.06381.58811.5608-0.0544-0.0097-0.09920.0328-0.04450.0932-0.01490.02230.09890.0062-0.00790.00940.0557-0.02920.038522.16729.87643.4547
22.987-0.1367-1.57960.7981-0.2351.6535-0.00940.0188-0.142-0.0668-0.1119-0.0403-0.00050.02830.12130.03310.01390.00530.01640.00580.010819.030531.7393-32.5883
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A265 - 479
2X-RAY DIFFRACTION2B265 - 481

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