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- PDB-1k4w: X-ray structure of the orphan nuclear receptor ROR beta ligand-bi... -

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Basic information

Entry
Database: PDB / ID: 1k4w
TitleX-ray structure of the orphan nuclear receptor ROR beta ligand-binding domain in the active conformation
Components
  • Nuclear receptor ROR-beta
  • steroid receptor coactivator-1
KeywordsHORMONE/GROWTH FACTOR / ligand-binding domain / alpha-helical sandwich / transcriptionally active conformation / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


retinal rod cell development / melatonin receptor activity / amacrine cell differentiation / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose ...retinal rod cell development / melatonin receptor activity / amacrine cell differentiation / retinal rod cell differentiation / retinal cone cell development / eye photoreceptor cell development / Nuclear Receptor transcription pathway / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor 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 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / 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 / cellular response to retinoic acid / response to retinoic acid / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / visual perception / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to hormone / response to progesterone / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / 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 / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / Circadian Clock / 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
STEARIC ACID / : / Nuclear receptor ROR-beta / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStehlin, C. / Wurtz, J.M. / Steinmetz, A. / Greiner, E. / Schuele, R. / Moras, D. / Renaud, J.P.
Citation
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.
#1: Journal: Hormones and Signaling / Year: 1998
Title: Nuclear orphan receptors: the search for novel ligands and signaling pathways
Authors: Willy, P.J. / Mangelsdorf, D.J.
#2: Journal: Endocr.Rev. / Year: 1999
Title: Orphan Nuclear Receptors: from Gene to Function
Authors: Giguere, V.
#3: Journal: Cell.Mol.Life Sci. / Year: 2000
Title: Structural Studies on Nuclear Receptors
Authors: Renaud, J.P. / Moras, D.
History
DepositionOct 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 21, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id ..._refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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-beta
B: steroid receptor coactivator-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9623
Polymers30,6782
Non-polymers2841
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-8 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.302, 58.489, 106.036
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: 28901.463 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: NR1F2 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P45446
#2: Protein/peptide steroid receptor coactivator-1


Mass: 1776.072 Da / Num. of mol.: 1 / Fragment: second NR-box / Source method: obtained synthetically
Details: The sequence of the protein was chemically synthesized. This sequence occurs naturally in humans.
References: GenBank: 1906028, UniProt: Q15788*PLUS
#3: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, NaCl, Tris.HCl, CHAPS, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris-HCl1reservoirpH8.0
215 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 6, 2000 / Details: Ge(220) focusing
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 28901 / Num. obs: 28901 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 29.8
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2837 / % possible all: 99.8
Reflection
*PLUS
Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.231

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LBD

2lbd


Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2372 9.9 %random
Rwork0.2238 ---
all-26336 --
obs-23854 90.6 %-
Displacement parametersBiso mean: 30.3 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 20 137 2223
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.282
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.1945 34 9.7 %
Rwork0.2048 --
obs-349 -
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor obs: 0.224 / Rfactor Rfree: 0.2494 / Rfactor Rwork: 0.2238
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.1945 / Rfactor Rwork: 0.2048

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