[English] 日本語
Yorodumi
- PDB-4mgd: Crystal structure of hERa-LBD (Y537S) in complex with HPTE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mgd
TitleCrystal structure of hERa-LBD (Y537S) in complex with HPTE
Components
  • (Estrogen receptor) x 2
  • Nuclear receptor coactivator 1
KeywordsHORMONE RECEPTOR / ligand-binding domain of nuclear hormone receptor
Function / homology
Function and homology information


labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / hypothalamus development ...labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / hypothalamus development / male mating behavior / prostate epithelial cord elongation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrous cycle / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / response to retinoic acid / histone acetyltransferase activity / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / lactation / nitric-oxide synthase regulator activity / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / hippocampus development / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / transcription coactivator binding / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation
Similarity search - Function
Nuclear receptor coactivator 1 / 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 1 / 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 / 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 / Zinc finger, C4 type (two domains) / 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
4,4'-(2,2,2-trichloroethane-1,1-diyl)diphenol / Estrogen receptor / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDelfosse, V. / Grimaldi, M. / Bourguet, W.
CitationJournal: Environ.Health Perspect. / Year: 2014
Title: Structural and functional profiling of environmental ligands for estrogen receptors.
Authors: Delfosse, V. / Grimaldi, M. / Cavailles, V. / Balaguer, P. / Bourguet, W.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
F: Nuclear receptor coactivator 1
G: Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0988
Polymers61,3084
Non-polymers7894
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-28 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.900, 81.880, 58.590
Angle α, β, γ (deg.)90.00, 110.54, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 29054.217 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29070.217 Da / Num. of mol.: 1 / Fragment: ligand binding domain (UNP residues 302-552) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372

-
Protein/peptide , 1 types, 2 molecules FG

#3: Protein/peptide Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: coactivator peptide SRC-1 (UNP residues 686-698) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788

-
Non-polymers , 4 types, 226 molecules

#4: Chemical ChemComp-27N / 4,4'-(2,2,2-trichloroethane-1,1-diyl)diphenol


Mass: 317.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11Cl3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 340 mM sodium chloride, 100 mM HEPES, 24% PEG3350, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→46.534 Å / Num. obs: 37978 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.085 / Net I/σ(I): 8.53
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.34 / Num. unique all: 2756 / Rsym value: 0.439 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UUD

3uud


Resolution: 1.9→46.534 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 26.11 / Stereochemistry target values: ML
Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO ESTROGEN RECEPTOR MOLECULES WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED ...Details: THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO ESTROGEN RECEPTOR MOLECULES WITH DISTINCT PATTERNS OF SIDE CHAIN MODIFICATION REPRESENTS THE BEST FIT TO THE ELECTRON DENSITY AND IS NOT DERIVED FROM THE CO-CRYSTALLIZATION OF TWO CHEMICALLY DISTINCT PROTEINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1898 5 %RANDOM
Rwork0.1961 ---
obs0.198 37961 99.19 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.147 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.1592 Å2-0 Å26.9726 Å2
2---0.3458 Å20 Å2
3----9.8133 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 48 222 4106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044013
X-RAY DIFFRACTIONf_angle_d0.7455452
X-RAY DIFFRACTIONf_dihedral_angle_d15.8471472
X-RAY DIFFRACTIONf_chiral_restr0.06654
X-RAY DIFFRACTIONf_plane_restr0.003676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94750.3081320.27892517X-RAY DIFFRACTION99
1.9475-2.00010.32381340.2552537X-RAY DIFFRACTION98
2.0001-2.0590.24651350.23462583X-RAY DIFFRACTION100
2.059-2.12540.30241360.20392585X-RAY DIFFRACTION100
2.1254-2.20140.25411350.20362574X-RAY DIFFRACTION99
2.2014-2.28950.28661380.20642606X-RAY DIFFRACTION100
2.2895-2.39370.24291350.19872568X-RAY DIFFRACTION99
2.3937-2.51990.26681340.20372546X-RAY DIFFRACTION99
2.5199-2.67780.27921360.21172592X-RAY DIFFRACTION100
2.6778-2.88450.29751360.2082573X-RAY DIFFRACTION99
2.8845-3.17470.22381350.20222573X-RAY DIFFRACTION99
3.1747-3.6340.21351360.19032585X-RAY DIFFRACTION99
3.634-4.57780.19131370.1682603X-RAY DIFFRACTION99
4.5778-46.5480.21011390.18912621X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more