[English] 日本語
Yorodumi
- PDB-7rnm: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rnm
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with 2-(2-Chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)isoindolin-5-ol and GRIP Peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Breast Cancer / Estrogen Receptor / Alpha Helical Bundle
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / 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 / uterus development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / 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 / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / calmodulin binding / protein dimerization activity / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / cytosol / cytoplasm
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, receptor-binding domain ...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, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / : / PAS domain / 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
Chem-61Z / Nuclear receptor coactivator 2 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJoiner, C. / Sammeta, V.K.R. / Norris, J.D. / McDonnell, D.P. / Willson, T.M. / Fanning, S.W.
CitationJournal: Helv.Chim.Acta / Year: 2023
Title: Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines
Authors: Reddy Sammeta, V. / Anderson, B.M. / Norris, J.D. / Torrice, C.D. / Joiner, C. / Liu, S. / Li, H. / Popov, K.I. / Fanning, S.W. / McDonnell, D.P. / Willson, T.M.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
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)60,1946
Polymers59,4344
Non-polymers7602
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-27 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.094, 83.456, 58.420
Angle α, β, γ (deg.)90.000, 108.520, 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: 28440.465 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


Mass: 1276.530 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2 / Production host: synthetic construct (others) / References: UniProt: E7EWM1
#3: Chemical ChemComp-61Z / 2-(2-chloro-5-phenylthieno[2,3-d]pyrimidin-4-yl)-2,3-dihydro-1H-isoindol-5-ol


Mass: 379.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MgCl2

-
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: Jul 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39739 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 1 / Net I/σ(I): 3785
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1935 / CC1/2: 0.576

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D0F

6d0f


Resolution: 1.9→46.44 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1804 5 %
Rwork0.1854 34262 -
obs0.1872 36066 90.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.54 Å2 / Biso mean: 27.0684 Å2 / Biso min: 5.8 Å2
Refinement stepCycle: final / Resolution: 1.9→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 52 378 3994
Biso mean--29.98 33.87 -
Num. residues----465
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.960.3648620.2735990105235
1.96-2.010.3187770.24781704178158
2.01-2.080.24591410.21452522266387
2.08-2.150.26141400.20122759289995
2.15-2.240.23731520.19182889304199
2.24-2.340.19261510.188728953046100
2.34-2.460.25221660.179828953061100
2.46-2.620.23331570.183229093066100
2.62-2.820.2331300.191329643094100
2.82-3.10.22871590.181529203079100
3.11-3.550.20461480.179929053053100
3.55-4.480.19631470.159429583105100
4.48-46.440.19661740.18932952312699
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)
12.8298-0.62710.61691.3654-1.02353.36680.0252-0.57720.19840.33760.0057-0.1146-0.30060.28860.31660.0679-0.0523-0.05310.2999-0.03760.160422.37056.621523.0944
22.1912-0.13751.29971.499-0.32481.7514-0.1208-0.187-0.2996-0.04450.11490.0510.0727-0.03090.01850.0970.00840.01040.11330.00880.05157.6403-1.334114.0347
36.70214.97581.85773.75131.01252.88430.09950.1017-0.2459-0.1919-0.15160.1332-0.2408-0.1747-0.03250.09210.060.01030.212-0.01220.2971-12.41616.439717.4412
45.4377-0.34025.7535.1026-2.35997.43820.18580.4942-0.964-1.05330.3482-0.06010.7791-0.1307-0.37180.6131-0.18210.04740.2729-0.06030.30118.555-14.314-10.6423
52.6785-1.6573-3.24035.64483.02726.32820.09430.0230.9510.326-0.17320.2387-0.7394-0.6417-0.06060.29390.04520.10760.1805-0.04370.3731-5.711918.192626.2418
64.20090.48431.60311.69440.17372.4459-0.05790.1924-0.5519-0.37230.2915-0.21190.08480.2783-0.07560.2298-0.01540.07560.3746-0.03130.186523.7506-0.8349-6.7403
73.19970.86880.69642.43790.56862.7313-0.0560.1513-0.224-0.22610.07970.09080.261-0.0118-0.01660.2424-0.03140.03730.1131-0.01690.090311.5161-3.3574-6.221
80.75130.7502-0.51131.4257-1.30363.092-0.11510.18690.3252-0.00910.19220.1714-0.7563-0.3022-0.33240.6965-0.0033-0.08920.22540.08130.20089.361916.312-8.3488
96.0334-0.37161.92543.1818-0.66483.8541-0.5171-0.15070.78230.61440.26590.1781-0.8578-0.22650.18350.45710.101-0.02830.15440.0060.250110.933814.64292.3563
103.5369-0.81471.45311.7780.82033.6545-0.05060.0823-0.1995-0.0784-0.0119-0.10830.1860.2530.0430.0806-0.00270.03630.1498-0.01850.102822.7719-1.78125.6445
114.89271.01891.77332.3090.57883.0863-0.2360.17710.2545-0.1570.05090.1691-0.2042-0.1810.19060.08710.01730.01720.10550.00490.05910.32284.84376.2583
122.21380.28150.7221.98570.10460.5910.1955-0.1113-0.29190.3537-0.14520.2029-0.1989-0.5365-0.07170.3845-0.0913-0.09580.42710.06230.3488-2.6865-4.081-9.1954
134.911.21170.00341.69360.2311.61970.0696-0.52720.37310.2703-0.06520.21560.00780.2133-0.04110.23840.01570.00970.1872-0.02850.11363.8651.301431.8372
146.93414.93061.33456.4671.50642.80950.1703-0.2328-0.09710.2564-0.11450.1842-0.1133-0.315-0.00910.08560.02440.04020.1307-0.00210.1421-5.18213.020727.0752
152.03630.369-0.26713.40960.00922.37010.0824-0.0378-0.04050.1202-0.06330.02430.04820.00230.02060.03850.00830.02370.0776-0.00010.08140.8086-0.283922.8238
163.0116-0.03193.59345.8904-0.09365.93790.03930.4572-0.3254-0.3221-0.1216-0.08910.30570.07780.01790.16230.00450.02870.1046-0.02510.14914.9146-10.750617.5795
173.52770.6045-0.37545.1552-0.21843.72930.028-0.1820.14870.13630.0836-0.1791-0.36440.2267-0.08290.0394-0.02530.03570.1047-0.03750.084912.20254.780521.3011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 474 through 496 )B474 - 496
2X-RAY DIFFRACTION2chain 'B' and (resid 497 through 530 )B497 - 530
3X-RAY DIFFRACTION3chain 'B' and (resid 531 through 547 )B531 - 547
4X-RAY DIFFRACTION4chain 'C' and (resid 688 through 695 )C688 - 695
5X-RAY DIFFRACTION5chain 'D' and (resid 688 through 696 )D688 - 696
6X-RAY DIFFRACTION6chain 'A' and (resid 307 through 340 )A307 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 394 )A341 - 394
8X-RAY DIFFRACTION8chain 'A' and (resid 395 through 421 )A395 - 421
9X-RAY DIFFRACTION9chain 'A' and (resid 422 through 438 )A422 - 438
10X-RAY DIFFRACTION10chain 'A' and (resid 439 through 496 )A439 - 496
11X-RAY DIFFRACTION11chain 'A' and (resid 497 through 530 )A497 - 530
12X-RAY DIFFRACTION12chain 'A' and (resid 531 through 547 )A531 - 547
13X-RAY DIFFRACTION13chain 'B' and (resid 307 through 338 )B307 - 338
14X-RAY DIFFRACTION14chain 'B' and (resid 339 through 363 )B339 - 363
15X-RAY DIFFRACTION15chain 'B' and (resid 364 through 420 )B364 - 420
16X-RAY DIFFRACTION16chain 'B' and (resid 421 through 437 )B421 - 437
17X-RAY DIFFRACTION17chain 'B' and (resid 438 through 473 )B438 - 473

+
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