[English] 日本語
Yorodumi
- PDB-6ln4: Estrogen-related receptor beta(ERR2) in complex with PGC1a-2a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ln4
TitleEstrogen-related receptor beta(ERR2) in complex with PGC1a-2a
Components
  • 10-mer from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
  • Steroid hormone receptor ERR2
KeywordsTRANSCRIPTION / ERR2 / Transcription factor / BPA
Function / homology
Function and homology information


cell dedifferentiation / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / regulation of stem cell division / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / stem cell division / : / negative regulation of stem cell differentiation / : ...cell dedifferentiation / positive regulation of mitochondrial DNA metabolic process / positive regulation of muscle tissue development / regulation of stem cell division / positive regulation of cellular respiration / positive regulation of fatty acid oxidation / stem cell division / : / negative regulation of stem cell differentiation / : / photoreceptor cell maintenance / cellular respiration / lncRNA binding / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / temperature homeostasis / nuclear steroid receptor activity / stem cell population maintenance / positive regulation of stem cell population maintenance / positive regulation of ATP biosynthetic process / response to starvation / RNA polymerase II complex binding / response to dietary excess / intracellular glucose homeostasis / fatty acid oxidation / inner ear development / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cis-regulatory region sequence-specific DNA binding / energy homeostasis / intracellular steroid hormone receptor signaling pathway / brown fat cell differentiation / condensed chromosome / positive regulation of gluconeogenesis / digestion / mitochondrion organization / respiratory electron transport chain / steroid binding / RNA splicing / nuclear receptor coactivator activity / SUMOylation of transcription cofactors / negative regulation of smooth muscle cell proliferation / gluconeogenesis / transcription initiation at RNA polymerase II promoter / nuclear receptor binding / transcription coregulator activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PML body / PPARA activates gene expression / chromatin DNA binding / mRNA processing / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / Circadian Clock / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / neuron apoptotic process / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / cell population proliferation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription coactivator activity / protein stabilization / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nuclear hormone receptor ...PGC-1alpha, RNA recognition motif / PGC-1 / Oestrogen-related receptor / Estrogen receptor/oestrogen-related receptor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding 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 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Steroid hormone receptor ERR2 / Peroxisome proliferator-activated receptor gamma coactivator 1-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Nov 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: 10-mer from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Theoretical massNumber of molelcules
Total (without water)27,3382
Polymers27,3382
Non-polymers00
Water97354
1
A: Steroid hormone receptor ERR2
B: 10-mer from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha

A: Steroid hormone receptor ERR2
B: 10-mer from Peroxisome proliferator-activated receptor gamma coactivator 1-alpha


Theoretical massNumber of molelcules
Total (without water)54,6764
Polymers54,6764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4360 Å2
ΔGint-27 kcal/mol
Surface area20070 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-9 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.472, 108.472, 106.902
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-541-

HOH

21A-544-

HOH

-
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: 26198.752 Da / Num. of mol.: 1 / Mutation: 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 Peroxisome proliferator-activated receptor gamma coactivator 1-alpha / PPARGC-1-alpha / Ligand effect modulator 6


Mass: 1139.319 Da / Num. of mol.: 1 / Mutation: C207A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPARGC1A, LEM6, PGC1, PGC1A, PPARGC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBK2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Kcl, 20% 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: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 12633 / % possible obs: 99.8 % / Redundancy: 24.5 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.029 / Rrim(I) all: 0.144 / Χ2: 0.96 / Net I/σ(I): 6.1 / Num. measured all: 309875
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.57-2.61110.6575920.9110.1820.6850.9397.4
2.61-2.6614.50.8246140.9360.2090.8520.86999.7
2.66-2.7118.10.7726090.9790.1810.7940.872100
2.71-2.7720.90.8566110.9680.1880.8770.841100
2.77-2.8324.20.7836210.9820.160.80.828100
2.83-2.8927.50.8616200.9760.1650.8770.83199.8
2.89-2.9727.90.7686180.9830.1470.7830.845100
2.97-3.0527.50.5836210.9940.1130.5940.883100
3.05-3.14260.4646200.9950.0930.4740.901100
3.14-3.2427.60.3776090.9950.0730.3840.895100
3.24-3.3529.30.326330.9970.060.3260.935100
3.35-3.4928.90.2426310.9980.0460.2460.998100
3.49-3.6527.70.2476340.9970.0480.2511.201100
3.65-3.8425.40.2156230.9930.0440.221.637100
3.84-4.0825.80.1546290.9970.0310.1571.208100
4.08-4.3926.90.1196480.9980.0240.1221.044100
4.39-4.84280.1026370.9990.020.1040.931100
4.84-5.53270.0956540.9980.0190.0970.845100
5.53-6.97250.096700.9980.0180.0920.771100
6.97-5020.50.0787390.9990.0180.080.82799.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E2R

2e2r


Resolution: 2.61→48.37 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 538 4.92 %
Rwork0.1983 10399 -
obs0.2005 10937 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.01 Å2 / Biso mean: 55.4122 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 2.61→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 0 54 1895
Biso mean---47.92 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.870.3023890.22711959204871
2.87-3.290.25541430.224727402883100
3.29-4.140.23481620.19292742290499
4.14-48.370.23611440.184329583102100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6327-0.41340.17135.10581.00995.83840.04690.27190.2563-0.67840.0155-0.0104-1.09010.5382-0.08790.5583-0.1431-0.01450.08880.03750.171-51.785610.7756-7.9736
24.22383.920.85632.0121.56594.252-0.13140.06141.1384-0.30910.0984-0.4308-0.75140.30860.07451.3996-1.0327-0.0074-0.5093-0.51140.6298-45.703927.2321.4035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 211:432)A211 - 432
2X-RAY DIFFRACTION2(chain B and resseq 207:216)B207 - 216

+
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://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