[English] 日本語
Yorodumi
- PDB-2yat: Crystal structure of estradiol derived metal chelate and estrogen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yat
TitleCrystal structure of estradiol derived metal chelate and estrogen receptor-ligand binding domain complex
ComponentsESTROGEN RECEPTOR
KeywordsTRANSCRIPTION
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 / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / negative regulation of canonical NF-kappaB signal transduction / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / : / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / : / 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 / 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
ESTRADIOL-PYRIDINIUM TETRAACETIC ACID / EUROPIUM ION / FORMIC ACID / Estrogen receptor
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsLi, M.J. / Greenblatt, H.M. / Dym, O. / Albeck, S. / Degani, H. / Sussman, J.L.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Structure of Estradiol Metal Chelate and Estrogen Receptor Complex: The Basis for Designing a New Class of Selective Estrogen Receptor Modulators.
Authors: Li, M.J. / Greenblatt, H.M. / Dym, O. / Albeck, S. / Pais, A. / Gunanathan, C. / Milstein, D. / Degani, H. / Sussman, J.L.
History
DepositionFeb 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references / Other ...Database references / Other / Structure summary / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6825
Polymers28,7741
Non-polymers9084
Water50428
1
A: ESTROGEN RECEPTOR
hetero molecules

A: ESTROGEN RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,36310
Polymers57,5482
Non-polymers1,8158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x+y,y,-z-1/31
Buried area3980 Å2
ΔGint-13 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.693, 64.693, 133.345
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

-
Components

#1: Protein ESTROGEN RECEPTOR / ESTROGEN RECEPTOR ALPHA / ER / ER-ALPHA / ESTRADIOL RECEPTOR / NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1


Mass: 28773.807 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 301-551 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Chemical ChemComp-EU / EUROPIUM ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu
#3: Chemical ChemComp-EEU / ESTRADIOL-PYRIDINIUM TETRAACETIC ACID


Mass: 663.714 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H41N3O10
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 381 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 417 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 381 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 417 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 530 TO SER
Sequence detailsHUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN SEQUENCE OF THIS STRUCTURE RANGES BETWEEN ...HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN SEQUENCE OF THIS STRUCTURE RANGES BETWEEN RESIDUES SER301 AND ALA551, WITH THREE MUTATIONS, C381S, C417S, AND C530S.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.49 % / Description: NONE
Crystal growpH: 7
Details: 20% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 5% TACSIMATE25, 0.1 M HEPES, PH 7.0.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2008
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10104 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 58.32 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 3.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P15

2p15


Resolution: 2.602→42.893 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 24.41 / Stereochemistry target values: ML / Details: RESIDUES 331-340, 414-422, 462-463 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2277 486 4.8 %
Rwork0.1821 --
obs0.1842 10065 99.92 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.373 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 68.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.2155 Å20 Å20 Å2
2--5.2155 Å20 Å2
3----10.4309 Å2
Refinement stepCycle: LAST / Resolution: 2.602→42.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 55 28 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091906
X-RAY DIFFRACTIONf_angle_d2.1332599
X-RAY DIFFRACTIONf_dihedral_angle_d15.704711
X-RAY DIFFRACTIONf_chiral_restr0.079299
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6016-2.9780.31670.22673137X-RAY DIFFRACTION100
2.978-3.75160.25171680.18043165X-RAY DIFFRACTION100
3.7516-42.89840.19911510.17373277X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0791.3456-0.45895.52731.91413.7677-0.5852-0.5125-0.78921.37680.30950.10021.0038-1.28770.23250.7113-0.4071-0.02340.55350.0870.521-17.5932-23.4011-10.9726
20.6132-1.0975-0.13551.6664-0.3354.7578-0.1207-0.1942-0.0568-0.05570.33670.23360.0561-1.7951-0.14620.2637-0.0031-0.07380.77450.04180.4139-19.7564-5.8906-13.6106
31.6598-1.025-1.72241.7393-0.16523.08040.04240.0896-0.20230.08390.01990.17570.119-0.438-0.0640.2745-0.07370.00150.28060.00540.3309-13.1755-9.9809-17.0237
40.5927-1.06110.45912.71490.36831.88320.26751.4994-0.607-0.81060.1618-0.39040.0852-0.7625-0.57460.44630.038-0.01241.10420.23880.5599-20.7045-3.8305-32.031
52.1608-1.8276-0.90192.0317-0.15231.52940.00530.4442-0.1094-0.2748-0.0432-0.0920.6217-0.60560.01420.4753-0.2264-0.030.4611-0.01960.338-11.7652-16.6718-24.8591
63.9903-0.17560.03022.2688-1.84288.92710.4729-0.4266-1.57990.0541.10310.4189-0.24022.3474-1.17960.65970.08010.15940.9741-0.00281.0773.2804-11.4172-5.546
72.31170.03771.13171.90642.45395.21620.4158-0.3161-0.31751.2948-0.0872-0.37832.27120.4843-0.19381.035-0.01130.09580.38980.02650.5622-2.4832-23.4808-9.3842
80.9863-0.1845-0.11140.2451-0.22880.6418-0.00120.3382-0.5962-0.1973-0.3865-0.04791.143-0.34640.26051.1162-0.26480.00970.388-0.12160.664-5.3406-31.7061-26.2872
92.8972-2.563-0.64765.3007-2.02362.04370.66860.58780.54780.1599-1.2412-0.6152-0.3904-0.00960.24690.271-0.0485-0.00620.31230.02780.3542-5.7319-4.2136-22.9085
106.48221.95972.33813.30063.1893.4476-0.1933-0.30071.09930.3896-0.4480.0078-1.3639-0.34380.54350.6635-0.0415-0.05620.48070.14070.5186-13.16.0728-13.1226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:28)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 29:68)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 69:106)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 107:125)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 126:156)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 157:168)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 169:190)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 191:206)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 207:231)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 232:248)

+
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://pdbjlvh1.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