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- PDB-7jym: CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(24... -

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Entry
Database: PDB / ID: 7jym
TitleCRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C (NHIS-RORGT(244-487)-L6-SRC1(678-692)) IN COMPLEX WITH A TRICYCLIC SULFONE INVERSE AGONIST
ComponentsNuclear receptor ROR-gamma, Nuclear receptor coactivator 1
KeywordsDNA BINDING PROTEIN/Agonist / RORGT / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVERSE AGONIST / DNA BINDING PROTEIN-Agonist complex
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 / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / labyrinthine layer morphogenesis ...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 / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / labyrinthine layer morphogenesis / negative regulation of thymocyte apoptotic process / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of fat cell differentiation / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / estrous cycle / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / lymph node development / adipose tissue development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / xenobiotic metabolic process / regulation of cellular response to insulin stimulus / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / hippocampus development / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / DNA-binding transcription repressor activity, RNA polymerase II-specific / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / response to estradiol / HATs acetylate histones / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
Similarity search - Domain/homology
Chem-Z8I / Nuclear receptor ROR-gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.051 Å
AuthorsSack, J.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Novel Tricyclic Pyroglutamide Derivatives as Potent ROR gamma t Inverse Agonists Identified using a Virtual Screening Approach.
Authors: Liu, Q. / Batt, D.G. / Weigelt, C.A. / Yip, S. / Wu, D.R. / Ruzanov, M. / Sack, J.S. / Wang, J. / Yarde, M. / Li, S. / Shuster, D.J. / Xie, J.H. / Sherry, T. / Obermeier, M.T. / Fura, A. / ...Authors: Liu, Q. / Batt, D.G. / Weigelt, C.A. / Yip, S. / Wu, D.R. / Ruzanov, M. / Sack, J.S. / Wang, J. / Yarde, M. / Li, S. / Shuster, D.J. / Xie, J.H. / Sherry, T. / Obermeier, M.T. / Fura, A. / Stefanski, K. / Cornelius, G. / Khandelwal, P. / Tino, J.A. / Macor, J.E. / Salter-Cid, L. / Denton, R. / Zhao, Q. / Dhar, T.G.M.
History
DepositionAug 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: 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, Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5882
Polymers32,8871
Non-polymers7011
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.297, 61.297, 155.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nuclear receptor ROR-gamma, Nuclear receptor coactivator 1 / 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 / SRC-1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 32886.922 Da / Num. of mol.: 1
Fragment: LIGAND-BINDING DOMAIN (UNP RESIDUES 265-508) FUSED TO SRC PEPTIDE (UNP RESIDUES 683-696),LIGAND-BINDING DOMAIN (UNP RESIDUES 265-508) FUSED TO SRC PEPTIDE (UNP RESIDUES 683-696)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG, NCOA1, BHLHE74, SRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51449, UniProt: Q15788
#2: Chemical ChemComp-Z8I / (3R,5S)-3-fluoro-5-[(3aR,9bR)-9b-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,2,3,3,3-heptafluoropropan-2-yl)-1,2,3a,4,5,9b-hexahydro-3H-benzo[e]indole-3-carbonyl]-1-(2-hydroxy-2-methylpropyl)pyrrolidin-2-one


Mass: 700.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H29F9N2O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20-26% PEG3350, 0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS PH 5.5-6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.051→57.05 Å / Num. obs: 6192 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 57.97 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.142 / Net I/σ(I): 17.4
Reflection shellResolution: 3.051→3.21 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 867 / Rsym value: 0.42 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vqf

6vqf


Resolution: 3.051→57.05 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.844 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.476
RfactorNum. reflection% reflectionSelection details
Rfree0.2637 311 5.06 %RANDOM
Rwork0.198 ---
obs0.2014 6143 100 %-
Displacement parametersBiso mean: 35.59 Å2
Baniso -1Baniso -2Baniso -3
1--5.8114 Å20 Å20 Å2
2---5.8114 Å20 Å2
3---11.6229 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 3.051→57.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 47 11 2110
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082175HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.882972HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d780SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2146HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion18.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion267SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1738SEMIHARMONIC4
LS refinement shellResolution: 3.051→3.12 Å
RfactorNum. reflection% reflection
Rfree0.3272 -7.32 %
Rwork0.2189 380 -
obs--100 %

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