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- PDB-9ecf: Crystal structure of the hERbeta LBD complexed with androstenedio... -

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Basic information

Entry
Database: PDB / ID: 9ecf
TitleCrystal structure of the hERbeta LBD complexed with androstenediol and SRC 2-2 peptide (crystal form 2)
Components
  • Estrogen receptor beta
  • Nuclear receptor coactivator 2
KeywordsNUCLEAR PROTEIN / nuclear receptor / transcription factor
Function / homology
Function and homology information


receptor antagonist activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts ...receptor antagonist activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor activity / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / 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 / positive regulation of DNA-binding transcription factor activity / Recycling of bile acids and salts / cellular response to hormone stimulus / transcription regulator inhibitor activity / estrogen receptor signaling pathway / steroid binding / : / positive regulation of adipose tissue development / 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 / ESR-mediated signaling / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / cellular response to estradiol stimulus / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / negative regulation of cell growth / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / : / cell-cell signaling / PIP3 activates AKT signaling / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / Extra-nuclear estrogen signaling / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 / Nuclear receptor coactivator 2 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 hERbeta LBD complexed with androstenediol and SRC 2-2 peptide
Authors: Pederick, J.L. / Bruning, J.B.
History
DepositionNov 14, 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

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Assembly

Deposited unit
E: Estrogen receptor beta
F: Estrogen receptor beta
G: Nuclear receptor coactivator 2
H: Nuclear receptor coactivator 2
A: Estrogen receptor beta
B: Estrogen receptor beta
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
I: Estrogen receptor beta
J: Estrogen receptor beta
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
M: Estrogen receptor beta
N: Estrogen receptor beta
O: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,51624
Polymers237,19316
Non-polymers2,3248
Water11,385632
1
E: Estrogen receptor beta
F: Estrogen receptor beta
G: Nuclear receptor coactivator 2
H: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8796
Polymers59,2984
Non-polymers5812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Estrogen receptor beta
B: Estrogen receptor beta
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8796
Polymers59,2984
Non-polymers5812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Estrogen receptor beta
J: Estrogen receptor beta
K: Nuclear receptor coactivator 2
L: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8796
Polymers59,2984
Non-polymers5812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
M: Estrogen receptor beta
N: Estrogen receptor beta
O: Nuclear receptor coactivator 2
P: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8796
Polymers59,2984
Non-polymers5812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.535, 108.381, 120.601
Angle α, β, γ (deg.)90.00, 104.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Estrogen receptor beta / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 28069.225 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92731
#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.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical
ChemComp-B81 / (3alpha,8alpha,17beta)-androst-5-ene-3,17-diol / 5-Androstenediol


Mass: 290.440 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H30O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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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: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→39.74 Å / Num. obs: 127984 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.072 / Rrim(I) all: 0.194 / Χ2: 1.02 / Net I/σ(I): 9.6 / Num. measured all: 907667
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.513 / Num. unique obs: 6261 / CC1/2: 0.291 / Rpim(I) all: 0.596 / Rrim(I) all: 1.627 / Χ2: 0.98 / % possible all: 98.8

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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→38.97 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 6406 5.01 %
Rwork0.2504 --
obs0.2517 127848 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13883 0 168 632 14683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214334
X-RAY DIFFRACTIONf_angle_d0.48319452
X-RAY DIFFRACTIONf_dihedral_angle_d13.8955184
X-RAY DIFFRACTIONf_chiral_restr0.0342409
X-RAY DIFFRACTIONf_plane_restr0.0042347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.36841990.38323975X-RAY DIFFRACTION99
2.02-2.050.39412140.36794030X-RAY DIFFRACTION98
2.05-2.070.36151970.36214038X-RAY DIFFRACTION99
2.07-2.10.37342120.35664001X-RAY DIFFRACTION99
2.1-2.130.36932030.33864067X-RAY DIFFRACTION99
2.13-2.150.34262190.32983982X-RAY DIFFRACTION100
2.15-2.190.3452390.31624007X-RAY DIFFRACTION99
2.19-2.220.33762060.32393984X-RAY DIFFRACTION99
2.22-2.250.37542160.30914089X-RAY DIFFRACTION99
2.25-2.290.32482530.30633947X-RAY DIFFRACTION99
2.29-2.330.3022100.28934062X-RAY DIFFRACTION99
2.33-2.370.27022360.28483992X-RAY DIFFRACTION99
2.37-2.420.33041910.28114051X-RAY DIFFRACTION99
2.42-2.470.30972100.27414052X-RAY DIFFRACTION99
2.47-2.520.29212070.26654013X-RAY DIFFRACTION99
2.52-2.580.32342070.26844064X-RAY DIFFRACTION100
2.58-2.640.28142440.26434033X-RAY DIFFRACTION99
2.64-2.710.32110.26054030X-RAY DIFFRACTION100
2.71-2.790.3052370.26694027X-RAY DIFFRACTION100
2.79-2.880.30332260.2514066X-RAY DIFFRACTION100
2.88-2.990.25722280.24234030X-RAY DIFFRACTION100
2.99-3.110.28462130.23594059X-RAY DIFFRACTION100
3.11-3.250.272240.24284069X-RAY DIFFRACTION100
3.25-3.420.26832120.22664061X-RAY DIFFRACTION100
3.42-3.630.22961990.21654098X-RAY DIFFRACTION100
3.63-3.910.23992230.20844083X-RAY DIFFRACTION100
3.91-4.310.20321820.20474124X-RAY DIFFRACTION100
4.31-4.930.24952320.19294085X-RAY DIFFRACTION100
4.93-6.210.22121750.23314154X-RAY DIFFRACTION100
6.21-38.970.2491810.22774169X-RAY DIFFRACTION99

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