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- PDB-1n4h: Characterization of ligands for the orphan nuclear receptor RORbeta -

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Basic information

Entry
Database: PDB / ID: 1n4h
TitleCharacterization of ligands for the orphan nuclear receptor RORbeta
Components
  • Nuclear Receptor ROR-beta
  • Steroid Receptor Coactivator-1Nuclear receptor coactivator 1
KeywordsHORMONE/GROWTH FACTOR / Alpha-helical sandwich / Protein-peptide-ligand complex / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


amacrine cell differentiation / retinal rod cell development / melatonin receptor activity / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...amacrine cell differentiation / retinal rod cell development / melatonin receptor activity / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / negative regulation of osteoblast differentiation / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / histone acetyltransferase activity / cellular response to retinoic acid / Recycling of bile acids and salts / regulation of cellular response to insulin stimulus / histone acetyltransferase / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / RORA activates gene expression / visual perception / lactation / Regulation of lipid metabolism by PPARalpha / cerebellum development / response to hormone / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear estrogen receptor binding / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / circadian rhythm / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / retina development in camera-type eye / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
RETINOIC ACID / : / Nuclear receptor ROR-beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStehlin-Gaon, C. / Willmann, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R.
Citation
Journal: Nat.Struct.Biol. / Year: 2003
Title: All-trans retinoic acid is a ligand for the orphan nuclear receptor RORbeta
Authors: Stehlin-Gaon, C. / Willmann, D. / Zeyer, D. / Sanglier, S. / Van Dorsselaer, A. / Renaud, J.-P. / Moras, D. / Schuele, R.
#1: Journal: Embo J. / Year: 2001
Title: X-Ray Structure Of The Orphan Nuclear Receptor RORbeta Ligand-Binding Domain In The Active Conformation
Authors: Stehlin, C. / Wurtz, J.M. / Steinmetz, A. / Greiner, E. / Schule, R. / Moras, D. / Renaud, J.P.
#2: Journal: Nature / Year: 1995
Title: Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid
Authors: Renaud, J.P. / Rochel, N. / Ruff, M. / Vivat, V. / Chambon, P. / Gronemeyer, H. / Moras, D.
History
DepositionOct 31, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear Receptor ROR-beta
B: Steroid Receptor Coactivator-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6703
Polymers31,3692
Non-polymers3001
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.199, 58.125, 106.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear Receptor ROR-beta / Nuclear receptor RZR-beta


Mass: 29593.297 Da / Num. of mol.: 1 / Fragment: Ligand-Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: RZR-beta / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / Tissue (production host): brain / References: UniProt: P45446
#2: Protein/peptide Steroid Receptor Coactivator-1 / Nuclear receptor coactivator 1


Mass: 1776.072 Da / Num. of mol.: 1 / Fragment: NR-2 box / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo Sapiens (human).
References: GenBank: 1906028, UniProt: Q15788*PLUS
#3: Chemical ChemComp-REA / RETINOIC ACID / Retinoic acid


Mass: 300.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: unknown / Details: Potier, N., (2003) Protein Sci., 12, 725.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976205 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976205 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 19390 / Observed criterion σ(I): 3
Reflection shellResolution: 2.1→2.17 Å
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 19344 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 8

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1k4W

1k4w


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.2547 16820 random
Rwork0.2174 --
all-19440 -
obs-19024 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.662 Å20 Å2-1.208 Å2
2--0 Å20 Å2
3---4.87 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 22 113 2201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_length_a0.007
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_angle_d1.1
X-RAY DIFFRACTIONc_improper_angle_d0.63
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ream.param
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63

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