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- PDB-4mgb: Crystal structure of hERa-LBD (Y537S) in complex with TCBPA -

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Basic information

Entry
Database: PDB / ID: 4mgb
TitleCrystal structure of hERa-LBD (Y537S) in complex with TCBPA
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE RECEPTOR / ligand-binding domain of nuclear hormone receptor
Function / homology
Function and homology information


labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity ...labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / histone H3K4 acetyltransferase activity / regulation of branching involved in prostate gland morphogenesis / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / histone H4K12 acetyltransferase activity / regulation of toll-like receptor signaling pathway / histone H4K16 acetyltransferase activity / nuclear estrogen receptor activity / histone H3K14 acetyltransferase activity / male mating behavior / histone H3K9 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K122 acetyltransferase activity / epithelial cell development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / hypothalamus development / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / androgen metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / estrous cycle / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / histone acetyltransferase / RNA polymerase II preinitiation complex assembly / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / positive regulation of DNA-binding transcription factor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / positive regulation of adipose tissue development / protein localization to chromatin / : / steroid binding / Regulation of lipid metabolism by PPARalpha / 14-3-3 protein binding / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / positive regulation of neuron differentiation / negative regulation of DNA-binding transcription factor activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / nitric-oxide synthase regulator activity / ESR-mediated signaling / TBP-class protein binding / cerebellum development / transcription coregulator binding / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling
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 / Nuclear receptor coactivators bHLH domain / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / 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'-propane-2,2-diylbis(2,6-dichlorophenol) / 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.
CitationJournal: Environ.Health Perspect. / Year: 2014
Title: Structural and functional profiling of environmental ligands for estrogen receptors.
Authors: Delfosse, V. / Grimaldi, M. / Cavailles, V. / Balaguer, P. / Bourguet, W.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 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: Nuclear receptor coactivator 1
D: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2258
Polymers61,3084
Non-polymers9164
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-30 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.670, 81.550, 58.720
Angle α, β, γ (deg.)90.00, 110.32, 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: 29054.217 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: pET32a / 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: 29070.217 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: pET32a / 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


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: coactivator peptide SRC-1 (UNP residues 686-698) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788

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Non-polymers , 3 types, 183 molecules

#4: Chemical ChemComp-XDH / 4,4'-propane-2,2-diylbis(2,6-dichlorophenol)


Mass: 366.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12Cl4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 320 mM sodium chloride, 100 mM HEPES, 30% PEG3350, pH 7.75, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→45.64 Å / Num. obs: 41002 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.087 / Net I/σ(I): 7.84
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.22 / Num. unique all: 6430 / Rsym value: 0.458 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UUD

3uud


Resolution: 1.85→45.636 Å / SU ML: 0.25 / σ(F): 2.01 / Phase error: 25.99 / Stereochemistry target values: ML
Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO ESTROGEN RECEPTOR MOLECULES WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO ESTROGEN RECEPTOR MOLECULES WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 2049 5 %random
Rwork0.2075 ---
obs0.2096 40985 99.31 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.24 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4824 Å2-0 Å27.6433 Å2
2--4.5723 Å20 Å2
3----8.0547 Å2
Refinement stepCycle: LAST / Resolution: 1.85→45.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3777 0 54 179 4010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043973
X-RAY DIFFRACTIONf_angle_d0.7645406
X-RAY DIFFRACTIONf_dihedral_angle_d16.0071436
X-RAY DIFFRACTIONf_chiral_restr0.051642
X-RAY DIFFRACTIONf_plane_restr0.003671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89320.32421340.28262531X-RAY DIFFRACTION97
1.8932-1.94060.28681350.26452573X-RAY DIFFRACTION100
1.9406-1.99310.32861350.24652565X-RAY DIFFRACTION99
1.9931-2.05170.26451370.23212596X-RAY DIFFRACTION100
2.0517-2.11790.23811370.21622594X-RAY DIFFRACTION100
2.1179-2.19360.27161370.21092599X-RAY DIFFRACTION100
2.1936-2.28140.26521370.21812607X-RAY DIFFRACTION100
2.2814-2.38530.29361370.22432596X-RAY DIFFRACTION100
2.3853-2.5110.30511360.21942602X-RAY DIFFRACTION100
2.511-2.66830.26031370.22082600X-RAY DIFFRACTION100
2.6683-2.87430.28381370.22392597X-RAY DIFFRACTION100
2.8743-3.16350.24571370.21212601X-RAY DIFFRACTION99
3.1635-3.62110.18871380.19582615X-RAY DIFFRACTION100
3.6211-4.56160.23581380.17992624X-RAY DIFFRACTION99
4.5616-45.64960.24651370.20282636X-RAY DIFFRACTION99

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