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- PDB-1tfc: CRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE ESTROGEN-RE... -

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Basic information

Entry
Database: PDB / ID: 1tfc
TitleCRYSTAL STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE ESTROGEN-RELATED RECEPTOR GAMMA IN COMPLEX WITH A STEROID RECEPTOR COACTIVATOR-1 PEPTIDE
Components
  • Estrogen-related receptor gamma
  • steroid receptor coactivator-1
KeywordsTRANSCRIPTION / TRANSCRIPTIONALLY ACTIVE CONFORMATION IN ABSENCE OF LIGAND
Function / homology
Function and homology information


AF-2 domain binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / hypothalamus development / male mating behavior / cellular response to Thyroglobulin triiodothyronine ...AF-2 domain binding / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear steroid receptor activity / hypothalamus development / male mating behavior / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / steroid binding / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / male gonad development / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / positive regulation of apoptotic process / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / 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 / 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 ...Oestrogen-related receptor / Retinoic acid receptor / 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 / Nuclear receptor coactivators bHLH domain / : / 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 / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 1KV6 refined to higher resolution / Resolution: 2.4 Å
AuthorsGreschik, H. / Flaig, R. / Renaud, J.P. / Moras, D.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structural Basis for the Deactivation of the Estrogen-related Receptor {gamma} by Diethylstilbestrol or 4-Hydroxytamoxifen and Determinants of Selectivity.
Authors: Greschik, H. / Flaig, R. / Renaud, J.P. / Moras, D.
#1: 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.
History
DepositionMay 27, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)60,3264
Polymers60,3264
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-27 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.477, 83.477, 239.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-20-

HOH

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Components

#1: Protein Estrogen-related receptor gamma / Estrogen receptor related protein 3 / ERR gamma-2


Mass: 28386.941 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: ESRRG, NR3B3, ERRG2, ERR3, KIAA0832 / 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 / 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: short chemically synthesized portion of naturally occuring steroid receptor coactivator-1
References: UniProt: Q15788
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 3.7 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TRIS.HCL, AMMONIUM SULFATE, GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 13, 2003 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND(111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 34152 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 54.9
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.284 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: 1KV6 refined to higher resolution
Starting model: PBD ENTRY 1KV6

1kv6


Resolution: 2.4→24.32 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1683 5.1 %RANDOM
Rwork0.243 ---
obs0.243 33223 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.63 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 72.9 Å2
Baniso -1Baniso -2Baniso -3
1-17.37 Å20 Å20 Å2
2--17.37 Å20 Å2
3----34.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-25 Å
Luzzati sigma a0.45 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 0 40 3739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_dihedral_angle_d20
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.413 153 4.9 %
Rwork0.355 2999 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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