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- PDB-4tv1: Crystal structure of hERa-LBD (Y537S) in complex with propylparaben -

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Basic information

Entry
Database: PDB / ID: 4tv1
TitleCrystal structure of hERa-LBD (Y537S) in complex with propylparaben
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHormone receptor / nuclear hormone receptor / ligand binding domain / endocrine disruptor / environmental compound
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / hypothalamus development / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / male mating behavior ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / hypothalamus development / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / protein localization to chromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / lactation / positive regulation of neuron differentiation / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / cerebellum development / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / hippocampus development / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding
Similarity search - Function
Nuclear receptor coactivator 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...Nuclear receptor coactivator 1 / Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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
propyl 4-hydroxybenzoate / DI(HYDROXYETHYL)ETHER / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
Funding support France, 1items
OrganizationGrant numberCountry
ANR CESA2010 CESA 004 02 France
CitationJournal: Acta Pharmacol.Sin. / Year: 2015
Title: A structural perspective on nuclear receptors as targets of environmental compounds.
Authors: Delfosse, V. / Maire, A.L. / Balaguer, P. / Bourguet, W.
History
DepositionJun 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,67015
Polymers60,5134
Non-polymers1,15711
Water4,918273
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-19 kcal/mol
Surface area18920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.890, 84.060, 58.360
Angle α, β, γ (deg.)90.00, 108.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28672.742 Da / Num. of mol.: 1 / Fragment: Residues 302-552 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 28656.742 Da / Num. of mol.: 1 / Fragment: Residues 302-552
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1 / Coactivator peptide SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: Residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS, histone acetyltransferase

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Non-polymers , 5 types, 284 molecules

#4: Chemical ChemComp-36M / propyl 4-hydroxybenzoate


Mass: 180.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12O3
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 300-340 mM NaCl, 100 mM Hepes, 24-32 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07231 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07231 Å / Relative weight: 1
ReflectionResolution: 1.85→46.4 Å / Num. obs: 43567 / % possible obs: 99.7 % / Redundancy: 7.4 % / Rsym value: 0.06 / Net I/σ(I): 20.53
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 5.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
PHENIX(phenix.refine: 1.6.4_486)phasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UUD

3uud


Resolution: 1.85→27.569 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 2177 5 %Random selection
Rwork0.1671 ---
obs0.1688 43551 99.84 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.395 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.979 Å2-0 Å24.2975 Å2
2--1.2003 Å2-0 Å2
3---0.7788 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 78 273 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064099
X-RAY DIFFRACTIONf_angle_d0.9665562
X-RAY DIFFRACTIONf_dihedral_angle_d18.3421546
X-RAY DIFFRACTIONf_chiral_restr0.064657
X-RAY DIFFRACTIONf_plane_restr0.003690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89020.24621340.21082551X-RAY DIFFRACTION100
1.8902-1.93420.24931370.19462584X-RAY DIFFRACTION100
1.9342-1.98250.24591350.18472568X-RAY DIFFRACTION100
1.9825-2.03610.24191350.17992569X-RAY DIFFRACTION100
2.0361-2.0960.22421360.17882596X-RAY DIFFRACTION100
2.096-2.16360.2331350.17272582X-RAY DIFFRACTION100
2.1636-2.24090.2091370.16992603X-RAY DIFFRACTION100
2.2409-2.33060.2081370.17042590X-RAY DIFFRACTION100
2.3306-2.43660.19741360.16732579X-RAY DIFFRACTION100
2.4366-2.5650.22631340.16322561X-RAY DIFFRACTION100
2.565-2.72560.181370.16722586X-RAY DIFFRACTION100
2.7256-2.93580.21071360.16622593X-RAY DIFFRACTION100
2.9358-3.23080.21071370.16722609X-RAY DIFFRACTION100
3.2308-3.69740.18341370.15632599X-RAY DIFFRACTION100
3.6974-4.65470.16631370.14152608X-RAY DIFFRACTION100
4.6547-27.5720.20581370.18412596X-RAY DIFFRACTION98

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