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- PDB-9ebg: Crystal structure of the hERalpha LBD complexed with androstenedi... -

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Basic information

Entry
Database: PDB / ID: 9ebg
TitleCrystal structure of the hERalpha LBD complexed with androstenediol and SRC 2-2 peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsNUCLEAR PROTEIN / nuclear receptor / transcription factor
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / 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 signaling by ERBB4 / : / : / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / cellular response to hormone stimulus / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / : / 14-3-3 protein binding / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / ESR-mediated signaling / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / 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
Similarity search - Domain/homology
(3alpha,8alpha,17beta)-androst-5-ene-3,17-diol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPederick, J.L. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100609 Australia
CitationJournal: To Be Published
Title: Crystal structure of the hERalpha LBD complexed with androstenediol and SRC 2-2 peptide
Authors: Pederick, J.L. / Bruning, J.B.
History
DepositionNov 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
A: Estrogen receptor
C: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3846
Polymers58,8034
Non-polymers5812
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.401, 83.401, 58.553
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 27821.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372
#3: Chemical ChemComp-B81 / (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol / 5-Androstenediol


Mass: 290.440 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C19H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 38.45 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: .1 M PIPES pH 7, 7% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→33.97 Å / Num. obs: 29803 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.028 / Rrim(I) all: 0.088 / Χ2: 0.99 / Net I/σ(I): 14.3 / Num. measured all: 293159
Reflection shellResolution: 2.02→2.07 Å / % possible obs: 98.4 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.872 / Num. measured all: 18882 / Num. unique obs: 2176 / CC1/2: 0.3 / Rpim(I) all: 0.311 / Rrim(I) all: 0.927 / Χ2: 0.74 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→33.97 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 36.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1472 4.94 %
Rwork0.2047 --
obs0.207 29783 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→33.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 42 132 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023933
X-RAY DIFFRACTIONf_angle_d0.3695347
X-RAY DIFFRACTIONf_dihedral_angle_d3.546520
X-RAY DIFFRACTIONf_chiral_restr0.03644
X-RAY DIFFRACTIONf_plane_restr0.003659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.38711480.3272547X-RAY DIFFRACTION98
2.09-2.160.2812970.28212573X-RAY DIFFRACTION99
2.16-2.250.32421200.25422591X-RAY DIFFRACTION100
2.25-2.350.30781560.25042531X-RAY DIFFRACTION100
2.35-2.470.25981100.2672621X-RAY DIFFRACTION100
2.47-2.630.3381300.26892581X-RAY DIFFRACTION100
2.63-2.830.28061500.25442570X-RAY DIFFRACTION100
2.83-3.110.28171320.24532577X-RAY DIFFRACTION100
3.12-3.560.24451340.21272586X-RAY DIFFRACTION100
3.57-4.490.21321480.15952567X-RAY DIFFRACTION100
4.5-33.970.20571470.1512567X-RAY DIFFRACTION100
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)
14.45821.6693-4.29929.54930.3025.50210.0521-1.26761.55550.2201-0.15351.4641-1.3186-0.43360.24310.52840.13110.10980.5054-0.15380.80281.0147-11.88317.9178
24.28480.75811.06983.30211.99964.01990.35520.1123-0.75080.60330.364-0.8240.47470.91360.56510.49360.1017-0.16470.3194-0.350.598914.1442-43.0947-32.5795
33.37493.2805-4.4223.3161-4.42735.92590.6160.42320.51551.4989-0.1059-0.3415-1.0006-0.0856-0.51130.52330.0159-0.14770.4281-0.08590.519926.2287-11.0335.9552
43.8299-0.66561.60561.83571.9923.67780.3904-0.8213-0.94680.8703-0.51550.50760.6933-0.16030.17820.6142-0.06290.13620.50220.01320.37958.9701-35.738912.783
51.73780.97990.46914.3284-1.02042.1912-0.2015-0.1753-0.16910.6244-0.23640.1993-0.0416-0.34040.20270.14750.00180.14890.3684-0.1140.34626.4784-26.65027.4654
64.1297-3.72474.11383.5797-2.80438.748-0.1271-0.58351.2979-0.5881-0.6243-0.8406-1.1357-0.16830.74180.62830.0052-0.01910.45040.01420.45412.6526-7.1051.8311
71.8978-1.164-0.3983.84121.19081.44760.07810.0659-0.1194-0.0737-0.21520.3371-0.0127-0.11930.12860.2268-0.01410.01660.3187-0.02820.224913.4887-32.558-0.2258
83.81070.8073-0.16531.92750.31582.9330.02470.0149-0.0354-0.1935-0.1410.0386-0.41440.01060.09980.2650.0134-0.06210.2271-0.05740.222820.1981-20.5324-6.5404
94.90620.2461-2.43084.5922-1.32813.2574-0.27440.0054-0.4389-0.11490.21331.2540.1313-1.65290.35090.34060.01620.02430.6133-0.09230.6129-3.3116-26.68041.3933
106.46940.21841.27826.26413.22886.25540.12550.1566-0.6255-0.8410.6259-1.5824-0.24810.6071-0.77920.3748-0.10250.14770.5114-0.07010.554732.1852-24.276-31.8537
111.48661.0268-2.49791.5949-1.37924.3412-0.66061.16030.0417-0.32550.45970.4723-0.2074-0.56830.12850.4511-0.1123-0.00310.4075-0.05920.30642.8091-21.0998-39.1371
124.72840.48052.1953.1792-0.70953.4299-0.04710.1138-0.0258-0.39540.1971-0.20480.01890.0514-0.07180.3066-0.0173-0.00740.3136-0.06710.22897.5965-28.7932-33.7496
133.3934-0.51971.02673.588-0.06813.6599-0.04940.3113-0.1153-0.0898-0.1098-0.3587-0.26380.15230.09280.21220.008-0.02380.2844-0.06690.249614.7434-26.6837-27.1179
143.53830.2749-1.04770.9527-1.31481.9741-0.13320.0596-0.0775-0.4025-0.00070.3667-0.3292-0.43710.03430.51520.2394-0.11590.569-0.12970.4414-2.2005-15.6592-28.8723
153.832-0.67391.64673.03640.32733.2778-0.3702-0.04320.28530.07360.1344-0.005-0.9551-0.00090.17550.49740.0461-0.07820.2596-0.04550.20715.3685-16.9207-23.2504
163.66951.28761.61344.37321.033581.1615-2.07470.77050.1315-0.8692-0.1210.4288-0.2769-0.29690.6193-0.0860.00110.7163-0.05260.506915.8181-39.1861-14.7794
172.97921.98470.88871.54671.00614.7649-0.14320.5145-0.5619-0.04770.1209-0.68370.07220.9113-0.07110.33860.05830.03870.8472-0.10860.432731.0911-22.6295-20.1152
187.33132.81.39791.62390.5192.2611-0.1058-0.3262-0.1996-0.01690.0077-0.0416-0.1398-0.32170.12610.29190.0389-0.02360.3084-0.01390.187713.5873-21.1333-17.2226
197.78040.92040.05713.1346-0.00184.66610.51630.1246-0.7062-0.50330.1870.10320.7844-0.9146-0.64090.4161-0.1193-0.06430.45370.03140.46590.6755-36.0971-27.5247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 12 )
2X-RAY DIFFRACTION2chain 'D' and (resid 3 through 10 )
3X-RAY DIFFRACTION3chain 'A' and (resid 309 through 321 )
4X-RAY DIFFRACTION4chain 'A' and (resid 322 through 338 )
5X-RAY DIFFRACTION5chain 'A' and (resid 339 through 363 )
6X-RAY DIFFRACTION6chain 'A' and (resid 364 through 371 )
7X-RAY DIFFRACTION7chain 'A' and (resid 372 through 437 )
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 530 )
9X-RAY DIFFRACTION9chain 'A' and (resid 531 through 548 )
10X-RAY DIFFRACTION10chain 'C' and (resid 309 through 321 )
11X-RAY DIFFRACTION11chain 'C' and (resid 322 through 338 )
12X-RAY DIFFRACTION12chain 'C' and (resid 339 through 363 )
13X-RAY DIFFRACTION13chain 'C' and (resid 364 through 405 )
14X-RAY DIFFRACTION14chain 'C' and (resid 406 through 421 )
15X-RAY DIFFRACTION15chain 'C' and (resid 422 through 455 )
16X-RAY DIFFRACTION16chain 'C' and (resid 456 through 471 )
17X-RAY DIFFRACTION17chain 'C' and (resid 472 through 496 )
18X-RAY DIFFRACTION18chain 'C' and (resid 497 through 530 )
19X-RAY DIFFRACTION19chain 'C' and (resid 531 through 548 )

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