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- PDB-1x7b: CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH ERB-041 -

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Basic information

Entry
Database: PDB / ID: 1x7b
TitleCRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH ERB-041
Components
  • Estrogen receptor beta
  • STEROID RECEPTOR COACTIVATOR-1
KeywordsTRANSCRIPTION / ESTROGEN RECEPTOR / ESTROGEN RECEPTOR BETA / ER-BETA / ER / ESTROGEN / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / AGONIST
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / cellular response to estrogen stimulus / estrogen response element binding / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / positive regulation of DNA-binding transcription factor activity ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / cellular response to estrogen stimulus / estrogen response element binding / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / positive regulation of DNA-binding transcription factor activity / negative regulation of cell growth / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / 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 / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-041 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsManas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. ...Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Structure-Based Design of Estrogen Receptor-Beta Selective Ligands
Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. ...Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C.
History
DepositionAug 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor beta
B: Estrogen receptor beta
C: STEROID RECEPTOR COACTIVATOR-1
D: STEROID RECEPTOR COACTIVATOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5346
Polymers56,9914
Non-polymers5422
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-42 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.181, 87.981, 99.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 27109.143 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, NR3A2, ESTRB / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q92731
#2: Protein/peptide STEROID RECEPTOR COACTIVATOR-1


Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence was derived from steroid receptor coactivator-1
#3: Chemical ChemComp-041 / 2-(3-FLUORO-4-HYDROXYPHENYL)-7-VINYL-1,3-BENZOXAZOL-5-OL


Mass: 271.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10FNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.6 Å3/Da / Density % sol: 0.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, Mg Formate, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 20994 / Num. obs: 19756 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.09 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 20.39
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1953 / Rsym value: 0.335 / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPLEX STRUCTURE OF ER-BETA WITH GENESTEIN.

Resolution: 2.3→14.96 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2306377.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.266 935 4.8 %RANDOM
Rwork0.218 ---
all0.223 21004 --
obs0.219 19285 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.1179 Å2 / ksol: 0.348253 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å20 Å20 Å2
2--3.5 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→14.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3740 0 40 140 3920
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs
2.3-2.440.3471364.50.2828913027
2.44-2.630.3411440.2593121
2.63-2.890.2971490.2513195
2.89-3.310.3141670.2533279
3.31-4.150.2511790.2033315
4.15-150.2191600.1833348
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4041.PAR041.TOP

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