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- PDB-9d8q: Crystal structure of Estrogen Receptor alpha from Melanotaenia fl... -

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Basic information

Entry
Database: PDB / ID: 9d8q
TitleCrystal structure of Estrogen Receptor alpha from Melanotaenia fluviatilis bound to estradiol and human SRC2 peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsNUCLEAR PROTEIN / transcription / nuclear receptor / estrogen / steroid
Function / homology
Function and homology information


RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / hormone binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / hormone binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / : / positive regulation of adipose tissue development / steroid binding / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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
ESTRADIOL / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesMelanotaenia fluviatilis (Murray River rainbowfish)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.751 Å
AuthorsMcDougal, D.P. / Pederick, J.L. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230100609 Australia
CitationJournal: To Be Published
Title: Structural basis of constraint in estrogen receptors
Authors: McDougal, D.P. / Pederick, J.L. / Shearwin-Whyatt, L. / Grutzner, F. / Bruning, J.B.
History
DepositionAug 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,4363
Polymers30,1642
Non-polymers2721
Water1448
1
A: Estrogen receptor
B: Nuclear receptor coactivator 2
hetero molecules

A: Estrogen receptor
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8726
Polymers60,3274
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area6120 Å2
ΔGint-28 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.184, 167.184, 167.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-704-

HOH

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Components

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


Mass: 28583.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Melanotaenia fluviatilis (Murray River rainbowfish)
Gene: ESR1 / Production host: Escherichia coli (E. coli) / References: UniProt: D6N7U3
#2: 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.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.23 Å3/Da / Density % sol: 61.89 % / Description: cubic
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 9-10% Tacsimate pH 7.0, 22% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 21, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→48.26 Å / Num. obs: 10699 / % possible obs: 100 % / Redundancy: 40.1 % / CC1/2: 1 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.025 / Rrim(I) all: 0.16 / Χ2: 1.01 / Net I/σ(I): 25.4 / Num. measured all: 428751
Reflection shellResolution: 2.75→2.9 Å / % possible obs: 100 % / Redundancy: 42.3 % / Rmerge(I) obs: 3.586 / Num. measured all: 64840 / Num. unique obs: 1533 / CC1/2: 0.689 / Rpim(I) all: 0.555 / Rrim(I) all: 3.629 / Χ2: 1.01 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIXv1.19.2refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.751→44.68 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2611 --
Rwork0.2264 --
obs-10684 99.91 %
Refinement stepCycle: LAST / Resolution: 2.751→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 20 8 1905

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