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- PDB-3uuc: Crystal structure of hERa-LBD (wt) in complex with bisphenol-C -

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Basic information

Entry
Database: PDB / ID: 3uuc
TitleCrystal structure of hERa-LBD (wt) in complex with bisphenol-C
ComponentsEstrogen receptor
KeywordsHORMONE RECEPTOR / Ligand-binding domain of nuclear hormone receptor
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Double treble clef zinc finger, C4 type / 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
4,4'-(2,2-dichloroethene-1,1-diyl)diphenol / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural and mechanistic insights into bisphenols action provide guidelines for risk assessment and discovery of bisphenol A substitutes.
Authors: Delfosse, V. / Grimaldi, M. / Pons, J.L. / Boulahtouf, A. / le Maire, A. / Cavailles, V. / Labesse, G. / Bourguet, W. / Balaguer, P.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9928
Polymers114,8674
Non-polymers1,1254
Water6,143341
1
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9964
Polymers57,4342
Non-polymers5622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-10 kcal/mol
Surface area19870 Å2
MethodPISA
2
C: Estrogen receptor
hetero molecules

D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9964
Polymers57,4342
Non-polymers5622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2890 Å2
ΔGint-8 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.530, 58.640, 93.020
Angle α, β, γ (deg.)75.64, 74.77, 62.82
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28716.840 Da / Num. of mol.: 4 / Fragment: Ligand binding domain (residues 302-552)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Chemical
ChemComp-0D1 / 4,4'-(2,2-dichloroethene-1,1-diyl)diphenol


Mass: 281.134 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10Cl2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM MgCl2, 100 mM BisTris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→46.9 Å / Num. all: 51238 / Num. obs: 51238 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 32.17 Å2 / Rsym value: 0.048 / Net I/σ(I): 10.49
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.82 / Num. unique all: 3745 / Rsym value: 0.425 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHENIXmodel building
PHENIX/ Refmacrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QXS

2qxs


Resolution: 2.1→46.897 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2548 2563 5 %Random
Rwork0.2136 ---
obs0.2157 51238 91.43 %-
all-51238 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.594 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.0627 Å2-0.7024 Å20.7955 Å2
2---5.3806 Å2-0.5428 Å2
3----1.6821 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7010 0 72 341 7423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077281
X-RAY DIFFRACTIONf_angle_d0.8919871
X-RAY DIFFRACTIONf_dihedral_angle_d16.3742642
X-RAY DIFFRACTIONf_chiral_restr0.0721171
X-RAY DIFFRACTIONf_plane_restr0.0041239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1-2.14040.31441410.27812682268291
2.1404-2.18410.34351380.27092613261389
2.1841-2.23160.32291360.26362586258686
2.2316-2.28350.27731420.24252688268892
2.2835-2.34060.28211450.23512763276392
2.3406-2.40390.29821400.232660266092
2.4039-2.47460.25911440.21592731273193
2.4746-2.55450.28251470.21942799279993
2.5545-2.64580.27581430.21842710271092
2.6458-2.75170.25511410.21892677267792
2.7517-2.87690.24981470.20512805280594
2.8769-3.02850.25371460.20032760276093
3.0285-3.21820.24671460.20642773277393
3.2182-3.46670.24931430.19962734273492
3.4667-3.81540.22751420.18942697269791
3.8154-4.36710.21381390.18432642264290
4.3671-5.50080.23091400.19742644264489
5.5008-46.90830.27941430.25282711271192

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