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- PDB-1lo1: ESTROGEN RELATED RECEPTOR 2 DNA BINDING DOMAIN IN COMPLEX WITH DNA -

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Basic information

Entry
Database: PDB / ID: 1lo1
TitleESTROGEN RELATED RECEPTOR 2 DNA BINDING DOMAIN IN COMPLEX WITH DNA
Components
  • 5'-D(*CP*GP*TP*GP*AP*CP*CP*TP*TP*GP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*CP*AP*AP*GP*GP*TP*CP*AP*CP*G)-3'
  • Steroid hormone receptor ERR2
KeywordsHORMONE/GROWTH FACTOR RECEPTOR/DNA / Estrogen Related Receptor 2 / DNA Binding Domain / hERR2 / Hormone Nuclear Receptor / HORMONE-GROWTH FACTOR RECEPTOR-DNA COMPLEX
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 / stem cell population maintenance / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / inner ear development ...cell dedifferentiation / regulation of stem cell division / stem cell division / negative regulation of stem cell differentiation / photoreceptor cell maintenance / nuclear steroid receptor activity / stem cell population maintenance / positive regulation of stem cell population maintenance / RNA polymerase II complex binding / inner ear development / estrogen response element binding / cis-regulatory region sequence-specific DNA binding / intracellular steroid hormone receptor signaling pathway / condensed chromosome / steroid binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell population proliferation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / 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 / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Oestrogen-related receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Estrogen receptor/oestrogen-related receptor / 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 ...Oestrogen-related receptor / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Estrogen receptor/oestrogen-related receptor / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Steroid hormone receptor ERR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsGearhart, M.D. / Holmbeck, S.M.A. / Evans, R.M. / Dyson, H.J. / Wright, P.E.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Monomeric Complex of Human Orphan Estrogen Related Receptor-2 with DNA: A Pseudo-dimer Interface Mediates Extended Half-site Recognition
Authors: Gearhart, M.D. / Holmbeck, S.M.A. / Evans, R.M. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*GP*CP*TP*CP*AP*AP*GP*GP*TP*CP*AP*CP*G)-3'
C: 5'-D(*CP*GP*TP*GP*AP*CP*CP*TP*TP*GP*AP*GP*C)-3'
A: Steroid hormone receptor ERR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2235
Polymers19,0923
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 32structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*GP*CP*TP*CP*AP*AP*GP*GP*TP*CP*AP*CP*G)-3'


Mass: 3976.599 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*GP*AP*CP*CP*TP*TP*GP*AP*GP*C)-3'


Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Steroid hormone receptor ERR2 / ERR-beta / Estrogen receptor-like 2 / estrogen-related receptor / beta


Mass: 11148.113 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN / Mutation: C163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hERR2 / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O95718
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1312D Filter Edit NOESY
1422D Filter Filter NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM hERR2 U-15N 13C, 0.5 mM DNA Strand 1, 0.5 mM DNA Strand 2, 20 mM K2SO4, 50 M ZnSO4, 2 mM dithiothreitol (DTT), 0.001% NaN3 pH 6.8100% D20
20.5 mM hERR2 U-15N, 0.5 mM DNA Strand 1, 0.5 mM DNA Strand 2, 20 mM K2SO4, 50 M ZnSO4, 2 mM dithiothreitol (DTT), 0.001% NaN3 pH 6.85% D2O, 95% H20
Sample conditionsIonic strength: 20 mM K2SO4 / pH: 6.8 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker DMXBrukerDMX7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.1F.Delaglio, S.Grzesiek, G.W.Vuister, Z.Guang, J.Pfeifer, A.Baxprocessing
NMRView4.1.3B.A.Johnson, R.A.Blevinsdata analysis
Amber6D.A.Case, D.A.Pearlman, et.al.refinement
DYANA1.5P.Gntert, C.Mumenthaler, K.Wthrichrefinement
Amber6D.A.Case, D.A.Pearlman, J.W.Caldwell, T.E.Cheatham III, W.S.Ross, C.L.Simmerling, T.A.Darden, K.M.Merz, R.V.Stanton, A.L.Cheng, J.J.Vincent, M.Crowley, V.Tsui, R.J.Radmer, Y.Duan, J.Pitera, I.Massova, G.L.Seibel, U.C.Singh, P.K.Weiner, and P.A.Kollmanstructure solution
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 32 / Conformers submitted total number: 20

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