[English] 日本語
Yorodumi
- PDB-6lit: Estrogen-related receptor beta(ERR2) in complex with BPA -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of stem cell division / stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / positive regulation of stem cell population maintenance / RNA polymerase II complex binding ...cell dedifferentiation / regulation of stem cell division / stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / nuclear steroid receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / stem cell population maintenance / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / locomotor rhythm / aryl hydrocarbon receptor binding / inner ear development / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / condensed chromosome / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / steroid binding / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / HATs acetylate histones / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding / transcription coactivator activity / nuclear body / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / regulation of transcription by RNA polymerase II / 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 / 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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more