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- PDB-1ere: HUMAN ESTROGEN RECEPTOR LIGAND-BINDING DOMAIN IN COMPLEX WITH 17B... -

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Basic information

Entry
Database: PDB / ID: 1ere
TitleHUMAN ESTROGEN RECEPTOR LIGAND-BINDING DOMAIN IN COMPLEX WITH 17BETA-ESTRADIOL
ComponentsESTROGEN RECEPTOR
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / STEROID / AGONIST
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / 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 / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / 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 / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / 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 / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / 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
ESTRADIOL / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBrzozowski, A.M. / Pike, A.C.W.
CitationJournal: 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
DepositionSep 8, 1997Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
C: ESTROGEN RECEPTOR
D: ESTROGEN RECEPTOR
E: ESTROGEN RECEPTOR
F: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,96812
Polymers173,3346
Non-polymers1,6346
Water2,054114
1
A: ESTROGEN RECEPTOR
B: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3234
Polymers57,7782
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-16 kcal/mol
Surface area18160 Å2
MethodPISA
2
C: ESTROGEN RECEPTOR
D: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3234
Polymers57,7782
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-17 kcal/mol
Surface area18140 Å2
MethodPISA
3
E: ESTROGEN RECEPTOR
F: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3234
Polymers57,7782
Non-polymers5452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-15 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.480, 115.160, 137.380
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999934, -0.011368, -0.001295), (-0.0113, 0.998982, -0.043665), (0.00179, -0.043647, -0.999045)48.5917, 6.11938, 270.85248
2given(0.538111, -0.804191, 0.252417), (-0.79793, -0.582523, -0.154841), (0.27156, -0.118089, -0.955149)21.25395, 111.6801, 216.51074
3given(-0.52526, -0.822829, -0.216918), (0.812216, -0.560819, 0.160583), (-0.253784, -0.091837, 0.962891)110.68032, 29.66769, -29.99837
4given(-0.401994, 0.882047, -0.245751), (-0.882506, -0.44478, -0.152818), (-0.244098, 0.155445, 0.957211)40.36324, 107.43404, -85.98657
5given(0.377903, 0.905091, 0.194933), (0.894898, -0.411065, 0.173733), (0.237374, 0.108791, -0.965307)-38.77313, 19.1583, 163.39461

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Components

#1: Protein
ESTROGEN RECEPTOR / ESTROGEN RECEPTOR / ER-LBD / ER-ALPHA


Mass: 28889.021 Da / Num. of mol.: 6 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ENDOGENOUS LIGAND 17 BETA-ESTRADIOL / Source: (gene. exp.) Homo sapiens (human) / Gene: ER ALPHA / Plasmid: PEALPHA 35 / Gene (production host): ER ALPHA / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / Variant (production host): C1857 / References: UniProt: P03372
#2: Chemical
ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H24O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.72 Å3/Da / Density % sol: 55 %
Crystal growpH: 8.1
Details: 2.4M AMMONIUM FORMATE, 8% DIMETHYLSULPHOXIDE, 0.1M TRIS-HCL, PH 8.1
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-13 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
32.4 Mammonium formate1reservoir
48 %dimethylsulphoxide1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.916
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 11, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 33981 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Rsym value: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 3→3.15 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.448 / % possible all: 98.5
Reflection
*PLUS
Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.49
Details: BULK SOLVENT CORRECTION AND ANISOTROPIC SCALING WERE USED. PHASES FROM SIX-FOLD AVERAGING WERE INCLUDED AT ALL STAGES OF REFINEMENT. TIGHT NCS RESTRAINTS WERE MAINTAINED THROUGHOUT. ER-LBD ...Details: BULK SOLVENT CORRECTION AND ANISOTROPIC SCALING WERE USED. PHASES FROM SIX-FOLD AVERAGING WERE INCLUDED AT ALL STAGES OF REFINEMENT. TIGHT NCS RESTRAINTS WERE MAINTAINED THROUGHOUT. ER-LBD WAS CARBOXYMETHYLATED PRIOR TO CRYSTALLIZATION BUT MODIFIED CYSTEINES ARE NOT MODELLED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3398 10 %RANDOM
Rwork0.218 ---
obs-33981 99.1 %-
Displacement parametersBiso mean: 57.48 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11262 0 120 114 11496
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4722
X-RAY DIFFRACTIONp_mcangle_it2.5943
X-RAY DIFFRACTIONp_scbond_it1.8462
X-RAY DIFFRACTIONp_scangle_it3.1733
X-RAY DIFFRACTIONp_plane_restr0.030.04
X-RAY DIFFRACTIONp_chiral_restr0.1180.15
X-RAY DIFFRACTIONp_singtor_nbd0.2080.3
X-RAY DIFFRACTIONp_multtor_nbd0.290.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor1.97
X-RAY DIFFRACTIONp_staggered_tor22.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS

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