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- PDB-5nu1: Structural states of RORgt: X-ray elucidation of molecular mechan... -

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Basic information

Entry
Database: PDB / ID: 5nu1
TitleStructural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor-interacting protein 1
KeywordsSIGNALING PROTEIN / nuclear hormone receptor / ligand-binding domain / inverse agonist
Function / homology
Function and homology information


ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage ...ovarian follicle rupture / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / nuclear glucocorticoid receptor binding / cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / lipid storage / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / histone deacetylase complex / regulation of glucose metabolic process / adipose tissue development / lymph node development / nuclear retinoid X receptor binding / xenobiotic metabolic process / SUMOylation of transcription cofactors / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / cellular response to estradiol stimulus / Heme signaling / circadian rhythm / Nuclear Receptor transcription pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / fibrillar center / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / transcription corepressor activity / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / nuclear speck / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / signaling receptor binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / Nuclear receptor ROR ...Nuclear receptor-interacting protein 1 / Nuclear receptor-interacting protein 1, repression domain 1 / Nuclear receptor-interacting protein 1, repression domain 2 / Nuclear receptor-interacting protein 1, repression domain 3 / Nuclear receptor-interacting protein 1, repression domain 4 / Nuclear receptor-interacting protein 1 repression 1 / Nuclear receptor-interacting protein 1 repression 2 / Nuclear receptor-interacting protein 1 repression 3 / Nuclear receptor-interacting protein 1 repression 4 / 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 / Double treble clef zinc finger, C4 type / 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
Chem-8YB / Nuclear receptor-interacting protein 1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsKallen, J.
CitationJournal: ChemMedChem / Year: 2017
Title: Structural States of ROR gamma t: X-ray Elucidation of Molecular Mechanisms and Binding Interactions for Natural and Synthetic Compounds.
Authors: Kallen, J. / Izaac, A. / Be, C. / Arista, L. / Orain, D. / Kaupmann, K. / Guntermann, C. / Hoegenauer, K. / Hintermann, S.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
P: Nuclear receptor-interacting protein 1
Q: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2376
Polymers64,1184
Non-polymers1,1192
Water4,342241
1
A: Nuclear receptor ROR-gamma
P: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6183
Polymers32,0592
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-9 kcal/mol
Surface area12670 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
Q: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6183
Polymers32,0592
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-9 kcal/mol
Surface area12580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.389, 68.802, 82.866
Angle α, β, γ (deg.)90.000, 102.920, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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: 29739.316 Da / Num. of mol.: 2 / Fragment: C-terminal domain, ligand binding domain / Mutation: C455S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P51449
#2: Protein/peptide Nuclear receptor-interacting protein 1 / Nuclear factor RIP140 / Receptor-interacting protein 140


Mass: 2319.615 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48552
#3: Chemical ChemComp-8YB / ~{N}-[4-(3-chlorophenyl)-5-(2-chlorophenyl)carbonyl-1,3-thiazol-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide


Mass: 559.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H20Cl2N2O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 23% PEG3350, 0.2M ammonium acetate, 0.1M bis-TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2016
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 1.85→19.76 Å / Num. obs: 45136 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.044 / Net I/σ(I): 20.6 / Num. measured all: 152690
Reflection shellResolution: 1.85→19.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.9 / Rrim(I) all: 0.495 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
REFMAC5refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NTI

5nti


Resolution: 1.85→19.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.116 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.156
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2257 5 %RANDOM
Rwork0.235 ---
obs0.2361 42878 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 55.14 Å2 / Biso mean: 27.925 Å2 / Biso min: 10.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.08 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.85→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 72 241 4453
Biso mean--21.23 32.32 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214345
X-RAY DIFFRACTIONr_angle_refined_deg0.911.9755873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1145517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76923.11209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0891534
X-RAY DIFFRACTIONr_chiral_restr0.0630.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023270
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 163 -
Rwork0.341 3110 -
all-3273 -
obs--99.85 %

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