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- PDB-4zi1: HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 4zi1
TitleHUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE
Components
  • Estrogen receptor beta
  • Nuclear receptor coactivator 5
KeywordsSIGNALING PROTEIN / ESTROGEN RECEPTOR BETA / BETA SELECTIVE / ERB
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / regulation of signal transduction / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / negative regulation of insulin receptor signaling pathway / steroid binding / ESR-mediated signaling ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / regulation of signal transduction / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / negative regulation of insulin receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / transcription corepressor activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / actin cytoskeleton / insulin receptor signaling pathway / PIP3 activates AKT signaling / cell-cell signaling / glucose homeostasis / 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 / 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 / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular space / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Anticodon-binding domain superfamily / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...: / Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Anticodon-binding domain superfamily / 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-KB0 / Estrogen receptor beta / Nuclear receptor coactivator 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKauppi, B. / Bonn, T.
CitationJournal: To Be Published
Title: HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE
Authors: Kauppi, B. / Bonn, T.
History
DepositionApr 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.title / _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: Estrogen receptor beta
B: Nuclear receptor coactivator 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6303
Polymers29,3162
Non-polymers3141
Water4,089227
1
A: Estrogen receptor beta
B: Nuclear receptor coactivator 5
hetero molecules

A: Estrogen receptor beta
B: Nuclear receptor coactivator 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2606
Polymers58,6314
Non-polymers6292
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area3430 Å2
ΔGint-28 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.258, 85.258, 112.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-818-

HOH

21A-905-

HOH

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Components

#1: Protein Estrogen receptor beta / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 28029.234 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP residues 262-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92731
#2: Protein/peptide Nuclear receptor coactivator 5 / NCoA-5 / Coactivator independent of AF-2 / CIA


Mass: 1286.430 Da / Num. of mol.: 1 / Fragment: 12mer PEPTIDE CIA12mod, UNP residues 341-352 / Mutation: Q343E, N347D / Source method: obtained synthetically
Details: Two mutations were made to increase peptide solubility
Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HCD5
#3: Chemical ChemComp-KB0 / 2-(4-hydroxyphenyl)-7-methyl-3-phenyl-1H-inden-5-ol / KB095285


Mass: 314.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCIA 12, 12-MER OF COACTIVATOR INDEPENDENT OF AF-2 FUNCTION PEPTIDE. DERIVED FROM NCOA5_HUMAN ...CIA 12, 12-MER OF COACTIVATOR INDEPENDENT OF AF-2 FUNCTION PEPTIDE. DERIVED FROM NCOA5_HUMAN RESIDUE NUMBER 341-352

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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: 3.6 Å3/Da / Density % sol: 65.1 % / Description: Bipyramides
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 10.5% (W/V) P6000, 1.75M NACL 0.1 M MES, PH 5.2, 12.5% (V/V) GLYCEROL, 2 TIMES EXCESS OF CIA12 PEPTIDE
PH range: 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→19.98 Å / Num. obs: 23165 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 2.47 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.87
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.24 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLM6.2.3data reduction
SCALA3.2.5data scaling
MOLREP8.2.01phasing
REFMAC5.1.9999refinement
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL DATA

Resolution: 2.1→19.98 Å / SU B: 7.075 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.149
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1193 5.15 %RANDOM
Rwork0.1747 ---
obs0.177 21970 99.13 %-
Displacement parametersBiso mean: 43.341 Å2
Baniso -1Baniso -2Baniso -3
1-0.758 Å20 Å20 Å2
2--0.758 Å20 Å2
3----1.516 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 24 227 2122
LS refinement shellHighest resolution: 2.1 Å

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