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- PDB-6ln4: Estrogen-related receptor beta(ERR2) in complex with PGC1a-2a -

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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 / regulation of stem cell division / Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration ...cell dedifferentiation / regulation of stem cell division / Regulation of MITF-M dependent genes involved in metabolism / positive regulation of fatty acid oxidation / stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / response to muscle activity / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / cellular respiration / lncRNA binding / nuclear steroid receptor activity / temperature homeostasis / stem cell population maintenance / positive regulation of stem cell population maintenance / response to starvation / RNA polymerase II complex binding / intracellular glucose homeostasis / fatty acid oxidation / response to dietary excess / inner ear development / cis-regulatory region sequence-specific DNA binding / estrogen response element binding / adipose tissue development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / brown fat cell differentiation / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / nuclear receptor-mediated steroid hormone signaling pathway / energy homeostasis / condensed chromosome / positive regulation of gluconeogenesis / digestion / steroid binding / respiratory electron transport chain / RNA splicing / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / mitochondrion organization / gluconeogenesis / nuclear receptor binding / transcription initiation at RNA polymerase II promoter / negative regulation of smooth muscle cell proliferation / transcription coregulator activity / circadian regulation of gene expression / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / PML body / chromatin DNA binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / mRNA processing / Regulation of RUNX2 expression and activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / positive regulation of cold-induced thermogenesis / cellular response to oxidative stress / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / neuron apoptotic process / negative regulation of neuron apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell population proliferation / 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 / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / 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 ...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

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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: 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

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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: 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


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Kcl, 20% 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: 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

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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

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