[English] 日本語
Yorodumi
- PDB-7jhd: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jhd
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with TTC-352 and GRIP Peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Breast Cancer / Synthetic Agonist / Drug Resistance / Apoptosis
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / regulation of lipid metabolic process / androgen metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / 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 / : / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 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 / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / 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 / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / 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 / PAS domain / Nuclear receptor coactivator, interlocking / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / 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 / 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
Similarity search - Domain/homology
Chem-V9J / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsFanning, S.W. / Abderraman, B. / Maximov, P.Y. / Jordan, V.C. / Greene, G.L.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: Rapid Induction of the Unfolded Protein Response and Apoptosis by Estrogen Mimic TTC-352 for the Treatment of Endocrine-Resistant Breast Cancer.
Authors: Abderrahman, B. / Maximov, P.Y. / Curpan, R.F. / Fanning, S.W. / Hanspal, J.S. / Fan, P. / Foulds, C.E. / Chen, Y. / Malovannaya, A. / Jain, A. / Xiong, R. / Greene, G.L. / Tonetti, D.A. / ...Authors: Abderrahman, B. / Maximov, P.Y. / Curpan, R.F. / Fanning, S.W. / Hanspal, J.S. / Fan, P. / Foulds, C.E. / Chen, Y. / Malovannaya, A. / Jain, A. / Xiong, R. / Greene, G.L. / Tonetti, D.A. / Thatcher, G.R.J. / Jordan, V.C.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 10, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0086
Polymers60,3034
Non-polymers7052
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-29 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.030, 82.436, 58.677
Angle α, β, γ (deg.)90.000, 110.750, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 28571.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, BHLHE75, SRC2, TIF2 / Production host: synthetic construct (others) / References: UniProt: Q15596
#3: Chemical ChemComp-V9J / 3-(4-fluorophenyl)-2-(4-hydroxyphenoxy)-1-benzothiophene-6-ol


Mass: 352.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H13FO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MgCl2, Tris HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.402→30.899 Å / Num. obs: 26664 / % possible obs: 92.8 % / Redundancy: 2.5 % / Rpim(I) all: 0.14 / Net I/σ(I): 172
Reflection shellResolution: 2.402→2.49 Å / Num. unique obs: 1321 / CC1/2: 0.561

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1Z

5t1z


Resolution: 2.402→30.899 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 969 5.17 %
Rwork0.2231 17765 -
obs0.2254 18734 65.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126 Å2 / Biso mean: 43.9783 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.402→30.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 50 123 3766
Biso mean--37.75 40.85 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023758
X-RAY DIFFRACTIONf_angle_d0.4955089
X-RAY DIFFRACTIONf_chiral_restr0.019605
X-RAY DIFFRACTIONf_plane_restr0.002629
X-RAY DIFFRACTIONf_dihedral_angle_d12.6551355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.42015-2.491230.3781380.292775920
2.5323-2.78690.31451600.2913299478
2.7869-3.18990.33121800.2649367294
3.1899-4.01750.2562080.2064370296
4.0175-100.21762220.1797365493
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)
10.36310.70160.10751.34310.21750.0309-0.13920.05780.3309-0.20750.13520.5561-0.2659-0.31030.16250.68840.6714-0.07360.36990.2990.4104-0.05669.8577-5.8677
25.5914-1.5552-0.92434.88910.26754.66430.0650.4133-0.2336-0.4644-0.0858-0.31270.15650.149-0.02050.2870.00660.10540.2336-0.02750.213320.1261-5.6311-2.8445
34.23882.0277-0.39163.32240.05932.85060.3113-0.11040.4377-0.285-0.3911-0.0008-0.6863-0.11450.08670.29150.02690.08740.2008-0.01780.25713.46344.22734.6712
43.65370.7218-1.31910.4716-1.09042.573-0.39850.4389-0.6152-0.3306-0.09140.37220.842-0.2180.41750.4643-0.02020.11760.2189-0.10930.360410.2085-15.6946-3.387
52.82830.18950.03161.02571.47722.219-0.1254-0.4812-0.89680.32210.05690.14941.19690.23850.06840.63160.0810.12840.1880.05360.359812.4554-17.97316.346
64.2889-0.9649-0.24930.5673-0.70971.86120.32360.16960.4639-0.3611-0.27190.2401-0.9754-0.6230.07430.37360.1662-0.00010.3404-0.01910.2165-0.40924.33313.815
74.9079-0.7231-1.78232.1690.25013.032-0.2738-0.2455-0.1650.07940.0114-0.24090.07390.24440.23340.25530.050.01510.18240.00420.128413.2178-4.894810.6214
80.5339-0.5241-0.01716.1772-1.0927.68090.2286-0.626-0.2394-0.29230.00951.2626-0.5692-1.9877-0.20530.27080.00990.08380.7713-0.12890.6503-17.2659-3.988725.9172
98.01323.34854.11875.28952.976.6289-1.2099-0.61210.0137-0.19990.5566-0.3804-0.6210.59260.50020.39210.09020.07570.4581-0.07120.30073.83791.137442.4559
104.99841.56021.18444.34532.96345.1494-0.8339-0.3606-0.56530.17840.3710.20710.61470.4417-0.13460.46620.01780.16530.27150.02630.32411.671-8.316934.7934
112.62510.4446-0.18351.4568-0.4272.6642-0.2649-0.1608-0.18610.0355-0.0291-0.07150.42040.23640.17680.33020.00610.10510.2019-0.01480.18693.3631-2.723429.136
124.44050.157-0.4522.05580.8115.7067-0.00730.02990.289-0.10840.2544-0.4763-1.0211.2529-0.25940.4401-0.13090.09380.4626-0.14170.336411.83638.574230.2413
134.69560.66041.24214.5334-0.21096.1307-0.04130.2819-0.1643-0.5098-0.0281-0.26630.0123-0.52110.06070.209-0.04640.03670.2555-0.03230.1882-4.1907-1.751622.099
143.4721-1.4001-0.68152.62450.26183.0771-0.2351-0.0197-0.1388-0.1249-0.01780.2575-0.2237-0.70790.11230.20910.0735-0.00590.2788-0.04150.1909-3.08120.548717.4833
151.88591.71123.0441.79711.97997.7213-0.8728-0.39830.07830.67490.0302-0.87510.21061.11720.38320.80990.374-0.01810.68280.1280.591915.1029-12.746433.5837
163.7512-0.85110.2161.86471.91285.19680.3989-0.59231.6964-0.0766-0.62280.0809-0.38761.03870.22870.5496-0.0910.30740.44170.00330.735524.766510.38431.343
170.7278-1.1912.11292.6287-3.62556.16710.2524-0.8768-1.22580.01190.1357-0.12590.9868-0.7967-0.12510.7442-0.22910.41520.35290.14530.70550.5961-19.878235.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 321 )A307 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 363 )A322 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 394 )A364 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 407 )A395 - 407
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 437 )A408 - 437
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 496 )A438 - 496
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 548 )A497 - 548
8X-RAY DIFFRACTION8chain 'B' and (resid 307 through 321 )B307 - 321
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 338 )B322 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 371 )B339 - 371
11X-RAY DIFFRACTION11chain 'B' and (resid 372 through 405 )B372 - 405
12X-RAY DIFFRACTION12chain 'B' and (resid 406 through 437 )B406 - 437
13X-RAY DIFFRACTION13chain 'B' and (resid 438 through 472 )B438 - 472
14X-RAY DIFFRACTION14chain 'B' and (resid 473 through 527 )B473 - 527
15X-RAY DIFFRACTION15chain 'B' and (resid 528 through 548 )B528 - 548
16X-RAY DIFFRACTION16chain 'C' and (resid 180 through 187 )C180 - 187
17X-RAY DIFFRACTION17chain 'D' and (resid 28 through 35 )D28 - 35

+
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