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- PDB-5jmm: Crystal structure of hERa-LBD (Y537S) in complex with biochanin A -

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Basic information

Entry
Database: PDB / ID: 5jmm
TitleCrystal structure of hERa-LBD (Y537S) in complex with biochanin A
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION / estrogen receptor / environmental ligand / isoflavone / endocrine disruptor
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
Chem-QSO / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDelfosse, V. / Bourguet, W.
Funding support France, 1items
OrganizationGrant numberCountry
ANSESEST-2013/1/031 France
CitationJournal: To Be Published
Title: Crystal structure of hERa-LBD (Y537S) in complex with biochanin A
Authors: Delfosse, V. / Bourguet, V.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: Nuclear receptor coactivator 1
G: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1239
Polymers61,3084
Non-polymers8155
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-26 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.400, 81.220, 58.170
Angle α, β, γ (deg.)90.00, 109.76, 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 / 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 BL21(DE3) (bacteria) / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372

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Protein/peptide , 1 types, 2 molecules FG

#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: UNP residues 686-698
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA1, BHLHE74, SRC1 / Production host: synthetic construct (others) / References: UniProt: Q15788, histone acetyltransferase

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Non-polymers , 4 types, 170 molecules

#4: Chemical ChemComp-QSO / 5,7-dihydroxy-3-(4-methoxyphenyl)-4H-chromen-4-one / Biochanin A


Mass: 284.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12O5
#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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.97 Å3/Da / Density % sol: 37.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 250 mM NaCl 100 mM Hepes 16% PEG3350 5% DMSO 10 mM b-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.977179 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977179 Å / Relative weight: 1
ReflectionResolution: 2.1→45.93 Å / Num. obs: 25312 / % possible obs: 90.6 % / Redundancy: 2.76 % / CC1/2: 0.998 / Rsym value: 0.056 / Net I/σ(I): 11.76
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2.25 % / Mean I/σ(I) obs: 2.09 / % possible all: 60.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UUA

3uua


Resolution: 2.1→45.93 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.91
RfactorNum. reflection% reflection
Rfree0.2161 1265 5 %
Rwork0.1654 --
obs0.168 25307 90.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 58 165 4021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074037
X-RAY DIFFRACTIONf_angle_d0.8265491
X-RAY DIFFRACTIONf_dihedral_angle_d16.3632459
X-RAY DIFFRACTIONf_chiral_restr0.045645
X-RAY DIFFRACTIONf_plane_restr0.004685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.18420.3222880.23641676X-RAY DIFFRACTION57
2.1842-2.28360.29641120.20862122X-RAY DIFFRACTION72
2.2836-2.4040.26641440.18592734X-RAY DIFFRACTION94
2.404-2.55460.25831520.18342900X-RAY DIFFRACTION99
2.5546-2.75180.2651520.17952890X-RAY DIFFRACTION99
2.7518-3.02860.2211550.17352928X-RAY DIFFRACTION99
3.0286-3.46680.22251530.16592911X-RAY DIFFRACTION99
3.4668-4.36720.19251540.13722921X-RAY DIFFRACTION99
4.3672-45.94470.17611550.15942960X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7581-0.3623-0.47710.7059-0.16132.0395-0.0488-0.1284-0.04830.03580.0023-0.00140.08860.0225-0.00020.157-0.010.00560.1324-0.01240.136512.3723.45880.2027
21.43820.0063-0.52821.07360.36141.0146-0.02330.0362-0.00890.0536-0.0305-0.03390.06840.0155-00.12470.0068-0.01410.11750.0080.11721.41062.9299-23.6553
30.13930.0464-0.05710.0312-0.07020.1893-0.1829-0.075-0.1591-0.0818-0.0491-0.07530.07720.0228-0.11980.420.09810.06940.18560.21660.36411.9494-14.54728.2851
40.0159-0.0037-0.04730.0602-0.00490.2966-0.01540.00190.1546-0.0677-0.0651-0.18620.05290.173-0.00860.0784-0.1302-0.02840.27630.05010.397636.000816.7231-25.9556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain F
4X-RAY DIFFRACTION4chain G

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