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- PDB-1gwq: HUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1gwq
TitleHUMAN OESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN COMPLEX WITH RALOXIFENE CORE AND TIF2 NRBOX2 PEPTIDE
Components
  • NUCLEAR RECEPTOR COACTIVATOR 2
  • OESTROGEN RECEPTOR
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / TRANSACTIVATION / AGONIST / AF2 COACTIVATOR / RECEPTOR / ACTIVATOR / TRANSCRIPTI REGULATION / DNA-BINDING / NUCLEAR PROTEIN / ZINC FINGER / STER BINDING / PHOSPHORYLATION / POLYMORPHISM / ALTERNATIVE SPLICIN
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / steroid hormone receptor signaling pathway / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear receptor-mediated steroid hormone signaling pathway / transcription regulator inhibitor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / positive regulation of adipose tissue development / steroid binding / : / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / peroxisome proliferator activated receptor signaling pathway / TBP-class protein binding / regulation of cellular response to insulin stimulus / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / response to progesterone / transcription corepressor binding / nuclear receptor binding / nuclear estrogen receptor binding / negative regulation of smoothened signaling pathway / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / 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 / transcription coactivator binding / euchromatin / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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
RALOXIFENE CORE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsPike, A.C.W. / Brzozowski, A.M.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Interaction of Transcriptional Intermediary Factor 2 Nuclear Receptor Box Peptides with the Coactivator Binding Site of Estrogen Receptor Alpha.
Authors: Warnmark, A. / Treuter, E. / Gustafsson, J.-A. / Hubbard, R.E. / Brzozowski, A.M. / Pike, A.C.W.
#1: Journal: Nature / Year: 1997
Title: Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor
Authors: Brzozowski, A.M. / Pike, A.C. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustafsson, J.A. / Carlquist, M.
History
DepositionMar 22, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 11, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OESTROGEN RECEPTOR
B: OESTROGEN RECEPTOR
C: NUCLEAR RECEPTOR COACTIVATOR 2
D: NUCLEAR RECEPTOR COACTIVATOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4986
Polymers59,0144
Non-polymers4852
Water2,144119
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-31 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.820, 63.620, 74.720
Angle α, β, γ (deg.)90.00, 98.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95729, 0.00948, 0.28897), (0.00943, -0.99995, 0.00158), (0.28897, 0.00121, -0.95734)
Vector: -4.27827, -0.19802, 29.09181)

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Components

#1: Protein OESTROGEN RECEPTOR / ER / ESTRADIOL RECEPTOR / ER-ALPHA


Mass: 28368.426 Da / Num. of mol.: 2 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 301-548
Source method: isolated from a genetically manipulated source
Details: LIGAND-BINDING DOMAIN (DOMAIN E - RESIDUES 260-500) IN COMPLEX WITH THE AGONIST RALOXIFENE CORE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEALPHA 35 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / Variant (production host): C1857 / References: UniProt: P03372
#2: Protein/peptide NUCLEAR RECEPTOR COACTIVATOR 2 / TRANSCRIPTION INTERMEDIARY FACTOR-2 / TIF2


Mass: 1138.383 Da / Num. of mol.: 2 / Fragment: NUCLEAR RECEPTOR BOX II, RESIDUES 688-696 / Source method: obtained synthetically
Details: TIF2 NR-BOX REGION 2 DERIVED PEPTIDE (RESIDUES 685-696)
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q15596
#3: Chemical ChemComp-ZTW / RALOXIFENE CORE


Mass: 242.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: 6-11% (W/V) PEG 1500, 4% (V/V) DMF, pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 19048 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 8 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 182603
Reflection shell
*PLUS
% possible obs: 93.9 % / Num. unique obs: 895

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERE

1ere


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN USED METHOD USED: BULK SOLVENT CONTRIBUTIONS CALCULATED BY XPLOR WERE ...Details: SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN USED METHOD USED: BULK SOLVENT CONTRIBUTIONS CALCULATED BY XPLOR WERE INCORPORATED IN THE FORM OF PARTIAL STRUCTURE FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 972 5 %RANDOM
Rwork0.206 ---
obs-17829 99.5 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3998 0 34 119 4151
LS refinement shellResolution: 2.45→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.343 104
Rwork0.248 -
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d0.036

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