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- PDB-6lit: Estrogen-related receptor beta(ERR2) in complex with BPA -

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Basic information

Entry
Database: PDB / ID: 6lit
TitleEstrogen-related receptor beta(ERR2) in complex with BPA
Components
  • 10-mer from Nuclear receptor coactivator 2
  • Steroid hormone receptor ERR2
KeywordsTRANSCRIPTION / ERR2 / Transcription factor / BPA
Function / homology
Function and homology information


cell dedifferentiation / morula formation / regulation of stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell division / stem cell population maintenance / locomotor rhythm / positive regulation of stem cell population maintenance ...cell dedifferentiation / morula formation / regulation of stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell division / stem cell population maintenance / locomotor rhythm / positive regulation of stem cell population maintenance / inner ear development / aryl hydrocarbon receptor binding / RNA polymerase II complex binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / somatic stem cell population maintenance / 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 / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / cis-regulatory region sequence-specific DNA binding / condensed chromosome / steroid binding / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / HATs acetylate histones / 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 / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / cell population proliferation / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 / cytoplasm / cytosol
Similarity search - Function
Oestrogen-related receptor / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / 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
Similarity search - Domain/homology
4,4'-PROPANE-2,2-DIYLDIPHENOL / Steroid hormone receptor ERR2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYao, B.Q. / Li, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770814 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Insights into the Specificity of Ligand Binding and Coactivator Assembly by Estrogen-Related Receptor beta.
Authors: Yao, B. / Zhang, S. / Wei, Y. / Tian, S. / Lu, Z. / Jin, L. / He, Y. / Xie, W. / Li, Y.
History
DepositionDec 13, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
A: Steroid hormone receptor ERR2
B: Steroid hormone receptor ERR2
D: 10-mer from Nuclear receptor coactivator 2
E: 10-mer from Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7766
Polymers55,3194
Non-polymers4572
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-21 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.951, 45.027, 57.368
Angle α, β, γ (deg.)84.310, 80.020, 79.310
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Steroid hormone receptor ERR2 / ERR beta-2 / Estrogen receptor-like 2 / Estrogen-related receptor beta / ERR-beta / Nuclear ...ERR beta-2 / Estrogen receptor-like 2 / Estrogen-related receptor beta / ERR-beta / Nuclear receptor subfamily 3 group B member 2


Mass: 26253.809 Da / Num. of mol.: 2 / Mutation: R382H,Y356H,Y215H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESRRB, ERRB2, ESRL2, NR3B2 / Production host: Escherichia coli (E. coli) / References: UniProt: O95718
#2: Protein/peptide 10-mer from Nuclear receptor coactivator 2 / SRC2-2b


Mass: 1405.710 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, BHLHE75, SRC2, TIF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15596
#3: Chemical ChemComp-2OH / 4,4'-PROPANE-2,2-DIYLDIPHENOL / 4,4'-ISOPROPYLIDENEDIPHENOL / BISPHENOL A


Mass: 228.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 300mM NH4Cl, 10% PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 25883 / % possible obs: 89.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.041 / Rrim(I) all: 0.058 / Χ2: 0.827 / Net I/σ(I): 11 / Num. measured all: 89330
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.631.80.11926020.9420.1190.1690.891.8
1.63-1.661.80.1126660.9530.110.1560.83192.5
1.66-1.691.80.10326320.9550.1030.1460.83891.8
1.69-1.721.80.09726100.9570.0970.1370.9192
1.72-1.761.80.08425580.9690.0840.1190.78991.1
1.76-1.81.70.07926880.970.0790.1110.83292.3
1.8-1.851.70.07326380.9730.0730.1030.83192.4
1.85-1.91.80.07126190.9710.0710.10.9391.2
1.9-1.951.80.06925310.9770.0690.0981.15588.1
1.95-2.021.80.05625920.9830.0560.0790.82691.6
2.02-2.091.70.05125770.9830.0510.0730.85290.5
2.09-2.171.60.04825920.9840.0480.0680.77990.9
2.17-2.271.70.04625270.9840.0460.0650.76387.9
2.27-2.391.80.04526090.9860.0450.0630.71690.2
2.39-2.541.80.04425480.9860.0440.0620.69290.2
2.54-2.741.70.04425660.9860.0440.0620.73289.9
2.74-3.011.70.04325930.9850.0430.060.70189.9
3.01-3.451.80.04324090.9880.0430.0610.75984.8
3.45-4.341.60.0422140.9890.040.0560.71978
4.34-301.80.0325250.9940.030.0421.03288.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E2R

2e2r


Resolution: 2→27.12 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2383 1368 5.29 %
Rwork0.1903 --
obs0.1928 25883 88.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.25 Å2 / Biso mean: 14.9179 Å2 / Biso min: 1.43 Å2
Refinement stepCycle: final / Resolution: 2→27.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 34 339 3756
Biso mean--9.91 20.28 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.28891360.18722558269491
2.07-2.150.221490.1792521267091
2.15-2.250.2411400.18062481262189
2.25-2.370.25211540.1812475262989
2.37-2.520.26261210.19362492261390
2.52-2.710.22661230.20152508263190
2.71-2.990.31381240.20682535265990
2.99-3.420.25151580.20592346250486
3.42-4.30.20191250.17812146227178
4.3-27.120.19871380.18542453259188

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