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- PDB-6fzu: RORGT (264-518;C455S) IN COMPLEX WITH THE FRAGMENT ("CPD-1") AND ... -

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Basic information

Entry
Database: PDB / ID: 6fzu
TitleRORGT (264-518;C455S) IN COMPLEX WITH THE FRAGMENT ("CPD-1") AND RIP140 PEPTIDE AT 1.80A
Components
  • Nuclear receptor ROR-gamma
  • Nuclear receptor-interacting protein 1
KeywordsTRANSCRIPTION / FBS / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVERSE AGONIST / SIGNALING PROTEIN
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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / ligand-activated transcription factor activity / lipid storage / Peyer's patch development ...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 / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / ligand-activated transcription factor activity / lipid storage / 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 / histone deacetylase complex / regulation of glucose metabolic process / lymph node development / adipose tissue development / nuclear retinoid X receptor binding / xenobiotic metabolic process / SUMOylation of transcription cofactors / cellular response to estradiol stimulus / nuclear receptor binding / nuclear estrogen receptor binding / circadian regulation of gene expression / Heme signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / fibrillar center / histone deacetylase binding / Nuclear Receptor transcription pathway / circadian rhythm / nuclear receptor activity / transcription corepressor activity / sequence-specific double-stranded DNA binding / Circadian Clock / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / signaling receptor binding / chromatin / regulation of transcription by RNA polymerase II / nucleolus / positive regulation of DNA-templated transcription / 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 / 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
~{N}-(3-chloranyl-4-ethoxy-phenyl)ethanamide / Nuclear receptor-interacting protein 1 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKallen, J.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Optimizing a Weakly Binding Fragment into a Potent ROR gamma t Inverse Agonist with Efficacy in an in Vivo Inflammation Model.
Authors: Carcache, D.A. / Vulpetti, A. / Kallen, J. / Mattes, H. / Orain, D. / Stringer, R. / Vangrevelinghe, E. / Wolf, R.M. / Kaupmann, K. / Ottl, J. / Dawson, J. / Cooke, N.G. / Hoegenauer, K. / ...Authors: Carcache, D.A. / Vulpetti, A. / Kallen, J. / Mattes, H. / Orain, D. / Stringer, R. / Vangrevelinghe, E. / Wolf, R.M. / Kaupmann, K. / Ottl, J. / Dawson, J. / Cooke, N.G. / Hoegenauer, K. / Billich, A. / Wagner, J. / Guntermann, C. / Hintermann, S.
History
DepositionMar 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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

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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)64,5456
Polymers64,1184
Non-polymers4272
Water4,792266
1
A: Nuclear receptor ROR-gamma
P: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2733
Polymers32,0592
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-8 kcal/mol
Surface area12620 Å2
MethodPISA
2
B: Nuclear receptor ROR-gamma
Q: Nuclear receptor-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2733
Polymers32,0592
Non-polymers2141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-9 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.918, 67.874, 82.451
Angle α, β, γ (deg.)90.000, 101.850, 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 (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-EE8 / ~{N}-(3-chloranyl-4-ethoxy-phenyl)ethanamide


Mass: 213.661 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12ClNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 22% 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: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 4, 2015
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.8 Å / Num. obs: 46451 / % possible obs: 96.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.652 / Rrim(I) all: 0.699 / % possible all: 93.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NTI

5nti


Resolution: 1.8→19.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.284 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1636 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.148
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 2323 5 %RANDOM
Rwork0.2148 ---
obs0.2166 44128 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 62.83 Å2 / Biso mean: 30.206 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-1.79 Å2
2--0.12 Å20 Å2
3----1.32 Å2
Refinement stepCycle: final / Resolution: 1.8→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 28 266 4444
Biso mean--40.39 38.25 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214277
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.965764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6675508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75923.11209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21115783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8371534
X-RAY DIFFRACTIONr_chiral_restr0.0750.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023200
LS refinement shellResolution: 1.802→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 164 -
Rwork0.285 3124 -
all-3288 -
obs--93.17 %

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