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- PDB-1kv6: X-ray structure of the orphan nuclear receptor ERR3 ligand-bindin... -

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Basic information

Entry
Database: PDB / ID: 1kv6
TitleX-ray structure of the orphan nuclear receptor ERR3 ligand-binding domain in the constitutively active conformation
Components
  • ESTROGEN-RELATED RECEPTOR GAMMA
  • steroid receptor coactivator 1Nuclear receptor coactivator 1
KeywordsGENE REGULATION / transcriptionally active conformation in absence of ligand / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


regulation of cellular response to drug / nuclear progesterone receptor binding / nuclear receptor binding => GO:0016922 / : / AF-2 domain binding / : / chromatin => GO:0000785 / bile acid and bile salt transport / labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway ...regulation of cellular response to drug / nuclear progesterone receptor binding / nuclear receptor binding => GO:0016922 / : / AF-2 domain binding / : / chromatin => GO:0000785 / bile acid and bile salt transport / 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 / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / estrogen response element binding / 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 / intracellular steroid hormone receptor signaling pathway / 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 / lactation / steroid binding / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / 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 / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / response to estradiol / positive regulation of cold-induced thermogenesis / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / neuron projection / positive regulation of apoptotic process / chromatin binding / chromatin / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Oestrogen-related receptor / Retinoic acid receptor / Helix-loop-helix DNA-binding domain / Nuclear receptor coactivator 1 / Estrogen receptor/oestrogen-related receptor / 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 ...Oestrogen-related receptor / Retinoic acid receptor / Helix-loop-helix DNA-binding domain / Nuclear receptor coactivator 1 / Estrogen receptor/oestrogen-related receptor / 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 / 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. / Nuclear receptor coactivator, interlocking / 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
Estrogen-related receptor gamma / Nuclear receptor coactivator 1 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGreschik, H. / Wurtz, J.-M. / Sanglier, S. / Bourguet, W. / van Dorsselaer, A. / Moras, D. / Renaud, J.-P. / Structural Proteomics in Europe (SPINE)
Citation
Journal: Mol.Cell / Year: 2002
Title: Structural and Functional Evidence for Ligand-Independent Transcriptional Activation by the Estrogen-Related Receptor 3
Authors: Greschik, H. / Wurtz, J.-M. / Sanglier, S. / Bourguet, W. / van Dorsselaer, A. / Moras, D. / Renaud, J.-P.
#1: Journal: Nature / Year: 1997
Title: Molecular basis of agonism and antagonism in the oestrogen receptor
Authors: Brzozowski, A.M. / Pike, A.C. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustafsson, J.A.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction with tamoxifen
Authors: Shiau, A.K. / Barstad, D. / Loria, P.M. / Cheng, L. / Agard, D.A. / Greene, G.L.
#3: 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. / Schuele, R. / Moras, D. / Renaud, J.P.
#4: Journal: Cell.Mol.Life Sci. / Year: 2000
Title: Structural studies on nuclear receptors
Authors: Renaud, J.P. / Moras, D.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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: ESTROGEN-RELATED RECEPTOR GAMMA
B: ESTROGEN-RELATED RECEPTOR GAMMA
C: steroid receptor coactivator 1
D: steroid receptor coactivator 1


Theoretical massNumber of molelcules
Total (without water)55,7214
Polymers55,7214
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.317, 83.317, 240.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: Protein ESTROGEN-RELATED RECEPTOR GAMMA / / ERR GAMMA-2 / nuclear receptor ERRG2 / estrogen-related receptor 3


Mass: 26084.373 Da / Num. of mol.: 2 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Details: complex with a SRC1 coactivator peptide in the absence of ligand
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3B3 / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62508
#2: Protein/peptide steroid receptor coactivator 1 / Nuclear receptor coactivator 1 / SRC-1 / nuclear receptor coactivator 1 / SRC-a/NCoA-1


Mass: 1776.072 Da / Num. of mol.: 2 / Fragment: second NR-box / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / References: UniProt: Q13420, UniProt: Q15788*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.04 Å3/Da / Density % sol: 69.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris.HCl, ammonium sulfate, glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMTris-HCl1reservoirpH8.0
31.5 Mammonium sulfate1reservoir
415 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2001 / Details: diamond(111) monochromator, Ge(220) focusing
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. obs: 23306 / % possible obs: 96.7 % / Biso Wilson estimate: 71 Å2 / Rsym value: 0.049
Reflection shellResolution: 2.7→2.81 Å / Num. unique all: 2587 / Rsym value: 0.148 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Rmerge(I) obs: 0.148

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBD ENTRY 3ERD

3erd


Resolution: 2.7→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2674 1038 4.8 %random
Rwork0.2328 ---
all-24019 --
obs-21641 90.1 %-
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 0 0 31 3691
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0136
X-RAY DIFFRACTIONc_angle_deg1.513
LS refinement shellResolution: 2.7→2.75 Å
RfactorNum. reflection
Rfree0.4406 43
Rwork0.3935 -
obs-860
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.233
Solvent computation
*PLUS
Displacement parameters
*PLUS

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