[English] 日本語
Yorodumi
- PDB-7kbs: Estrogen Receptor Alpha Ligand Binding Domain in Complex with Ral... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kbs
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with Raloxifene
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen Receptor / Breast Cancer / Selective Estrogen Receptor Modulator
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 / prostate epithelial cord 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 / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct 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 / : / : / 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 / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Regulation of RUNX2 expression and activity / 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 / cytosol / cytoplasm
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
RALOXIFENE / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.834 Å
AuthorsFanning, S.W.
CitationJournal: Elife / Year: 2022
Title: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
Authors: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
History
DepositionOct 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2894
Polymers60,3422
Non-polymers9472
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-13 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.802, 57.879, 87.950
Angle α, β, γ (deg.)90.000, 102.930, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 30171.119 Da / Num. of mol.: 2 / Fragment: Alpha Ligand Binding Domain, residues 307-554 / Mutation: L536S, C381S, C417S, C530S
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: Chemical ChemComp-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, MgCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.834→30.864 Å / Num. obs: 39139 / % possible obs: 89.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.01
Reflection shellResolution: 1.834→1.9 Å / Num. unique obs: 7108 / CC1/2: 0.6

-
Processing

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

5ufx


Resolution: 1.834→30.864 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 2030 5.19 %
Rwork0.1713 37109 -
obs0.1732 39139 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.99 Å2 / Biso mean: 23.226 Å2 / Biso min: 3.72 Å2
Refinement stepCycle: final / Resolution: 1.834→30.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 68 338 4150
Biso mean--18.45 31.66 -
Num. residues----476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073926
X-RAY DIFFRACTIONf_angle_d1.0055321
X-RAY DIFFRACTIONf_chiral_restr0.041618
X-RAY DIFFRACTIONf_plane_restr0.004659
X-RAY DIFFRACTIONf_dihedral_angle_d14.2141447
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.834-1.87660.3122780.2167136350
1.8766-1.92350.2603950.2092178165
1.9235-1.97550.22371270.2004207576
1.9755-2.03360.25031510.1911229583
2.0336-2.09930.2261120.1879248489
2.0993-2.17430.2341370.1683257493
2.1743-2.26130.21361480.1623259094
2.2613-2.36420.17321370.163265396
2.3642-2.48880.21951580.169271599
2.4888-2.64460.21761470.1647279199
2.6446-2.84870.20651590.1707273799
2.8487-3.13510.20021660.15892755100
3.1351-3.58820.21341550.1575276399
3.5882-4.51840.16131350.1527277298
4.5184-30.8640.23661250.197276195
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)
11.85260.85-0.51111.6474-0.16711.4271-0.02430.14290.04390.0994-0.0035-0.0332-0.1265-0.18110.0750.14410.0444-0.02470.12250.01260.184-2.6057-15.148424.5315
22.09370.9104-0.69831.5801-0.32621.47180.00180.134-0.0441-0.0094-0.06890.0641-0.0065-0.11340.01180.10790.0458-0.01310.1282-0.00680.1267-5.8444-25.172321.5447
31.41060.3239-0.17310.6131-0.34341.61-0.0108-0.0006-0.02390.0440.0145-0.0254-0.0179-0.0728-0.01650.09780.02930.00340.0698-0.00370.09544.5285-24.146727.0364
40.04540.0203-0.337-0.0222-0.03591.36030.01240.1772-0.2485-0.5362-0.16930.10530.4740.12010.07850.50120.04660.13040.40740.16360.475714.9065-27.96117.0261
51.40360.67060.69281.97791.41484.5515-0.01280.21780.1855-0.12320.0423-0.1358-0.1339-0.0062-0.00770.1460.0114-0.00080.15650.04090.159417.5148-12.915614.9897
61.92731.24460.31412.44420.22630.843-0.0153-0.0024-0.0490.0172-0.0168-0.04240.04340.08420.03030.09590.03140.01620.1027-0.00430.114813.6447-26.211426.6289
70.68360.2551-0.07372.0464-1.22672.0066-0.04770.3471-0.0494-0.61690.16210.47570.1575-0.16960.03660.2999-0.0513-0.05090.49620.02690.2265-5.3463-27.3988.4863
81.29370.08280.07811.858-0.0811.3059-0.01540.1389-0.0498-0.00420.0318-0.24440.14230.11970.08090.08940.01960.00860.17530.02610.152337.586-3822.8405
91.0370.27030.20072.61571.10121.90710.01330.006-0.1591-0.1775-0.0633-0.05480.00080.02490.01270.11390.0540.01670.13020.00390.140831.5347-44.96724.81
100.706-0.30270.01570.76630.22731.66150.0105-0.0283-0.01170.0495-0.02740.0088-0.0319-0.02470.00990.10330.0265-0.00150.10450.01360.10526.9561-36.27830.4899
111.3142-0.92970.18142.0987-1.19841.662-0.18210.45290.1889-0.78340.0358-0.2824-0.26430.392-0.00670.26360.16020.09950.29220.0460.119632.5473-39.00169.2008
121.6382-0.53020.24520.17090.02050.29810.03120.4668-0.3877-0.4357-0.16290.32580.2141-0.27090.07970.32810.1126-0.03750.4662-0.12470.251722.4067-46.17336.7804
132.32661.3650.25964.06480.43991.79180.11610.3572-0.0346-0.6428-0.23040.2311-0.2886-0.2729-0.00030.26230.1696-0.03750.39950.01710.058323.1407-33.1779.9744
141.1854-0.02060.23491.8778-0.02972.0030.14080.04780.08250.14810.00290.0801-0.2216-0.2502-0.06250.11380.04430.02480.11950.02460.159727.3883-27.875426.7341
151.48280.1252-0.55652.3323-1.15882.9291-0.0397-0.13820.14580.30210.06710.0165-0.00960.06760.00880.15330.006-0.03170.1347-0.01650.191229.2452-20.352632.3197
161.10681.04160.13743.6753-0.07370.48490.03280.09460.0292-0.1057-0.04370.1115-0.0013-0.0333-0.00740.10950.03310.0020.13150.00460.138320.7383-27.721819.6973
170.14940.26430.26470.36080.41110.38150.16870.1992-0.9222-0.40260.02870.52830.6269-0.1146-0.10910.3536-0.0003-0.09180.2548-0.04720.339618.7053-50.969326.0158
183.19181.59940.57353.95920.83573.7955-0.0604-0.2513-0.2828-0.0856-0.253-0.32980.27680.5826-0.00510.22680.01310.01950.20330.06630.109828.876-46.167338.7116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 338 )A307 - 338
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 363 )A339 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 455 )A364 - 455
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 465 )A456 - 465
5X-RAY DIFFRACTION5chain 'A' and (resid 466 through 496 )A466 - 496
6X-RAY DIFFRACTION6chain 'A' and (resid 497 through 528 )A497 - 528
7X-RAY DIFFRACTION7chain 'A' and (resid 529 through 550 )A529 - 550
8X-RAY DIFFRACTION8chain 'B' and (resid 306 through 341 )B306 - 341
9X-RAY DIFFRACTION9chain 'B' and (resid 342 through 363 )B342 - 363
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 394 )B364 - 394
11X-RAY DIFFRACTION11chain 'B' and (resid 395 through 407 )B395 - 407
12X-RAY DIFFRACTION12chain 'B' and (resid 408 through 421 )B408 - 421
13X-RAY DIFFRACTION13chain 'B' and (resid 422 through 437 )B422 - 437
14X-RAY DIFFRACTION14chain 'B' and (resid 438 through 466 )B438 - 466
15X-RAY DIFFRACTION15chain 'B' and (resid 467 through 496 )B467 - 496
16X-RAY DIFFRACTION16chain 'B' and (resid 497 through 527 )B497 - 527
17X-RAY DIFFRACTION17chain 'B' and (resid 528 through 536 )B528 - 536
18X-RAY DIFFRACTION18chain 'B' and (resid 537 through 546 )B537 - 546

+
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