[English] 日本語
Yorodumi
- PDB-6czn: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6czn
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Z2OHTPE and a glucocorticoid receptor-interacting protein 1 NR box II peptide
Components
  • Estrogen receptor
  • GRIP Peptide
KeywordsNUCLEAR PROTEIN / Estrogen Agonist / Breast Cancer / Nuclear Hormone Receptor
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / nuclear estrogen receptor activity / regulation of toll-like receptor signaling pathway / prostate epithelial cord elongation ...regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / nuclear estrogen receptor activity / regulation of toll-like 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 / epithelial cell development / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / cellular response to Thyroglobulin triiodothyronine / negative regulation of smooth muscle cell apoptotic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / regulation of lipid metabolic process / nuclear receptor-mediated steroid hormone signaling pathway / mammary gland alveolus development / : / cellular response to estrogen stimulus / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / : / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Mitochondrial unfolded protein response (UPRmt) / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / Recycling of bile acids and salts / positive regulation of nitric-oxide synthase activity / cellular response to hormone stimulus / estrogen receptor signaling pathway / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein localization to chromatin / peroxisome proliferator activated receptor signaling pathway / response to progesterone / 14-3-3 protein binding / BMAL1:CLOCK,NPAS2 activates circadian expression / regulation of cellular response to insulin stimulus / positive regulation of adipose tissue development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / nuclear receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / negative regulation of canonical NF-kappaB signal transduction / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / negative regulation of smoothened signaling pathway / Heme signaling / PPARA activates gene expression / Transcriptional activation of mitochondrial biogenesis / Cytoprotection by HMOX1 / euchromatin / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / mRNA transcription by RNA polymerase II / response to estrogen / beta-catenin binding / male gonad development / nuclear receptor activity / transcription coactivator binding / RNA polymerase II transcription regulator complex / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / ATPase binding / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / Nuclear receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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 / Nuclear receptor coactivators bHLH domain / 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 / 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
4,4'-[(1R,2R)-1-phenylbutane-1,2-diyl]diphenol / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFanning, S.W. / Han, R. / Maximov, P. / Jordan, V.C. / Greene, G.L.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain Y537S Mutant in Complex with Z2OHTPE and a glucocorticoid receptor-interacting protein 1 NR box II peptide
Authors: Fanning, S.W.
History
DepositionApr 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Oct 4, 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: GRIP Peptide
D: GRIP Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3966
Polymers61,7594
Non-polymers6372
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-30 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.837, 81.659, 58.381
Angle α, β, γ (deg.)90.00, 111.07, 90.00
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: 29299.535 Da / Num. of mol.: 2 / Mutation: Y537S
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 GRIP Peptide


Mass: 1579.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-FNJ / 4,4'-[(1R,2R)-1-phenylbutane-1,2-diyl]diphenol


Mass: 318.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H22O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.94 Å3/Da / Density % sol: 36.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3,350, 200 mM MgCl2, Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15539 / % possible obs: 89 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.52
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.95 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CBZ

6cbz


Resolution: 2.5→46.1 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 709 5.12 %
Rwork0.196 --
obs0.198 13838 84.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3397 0 48 62 3507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023524
X-RAY DIFFRACTIONf_angle_d0.5554768
X-RAY DIFFRACTIONf_dihedral_angle_d13.1621230
X-RAY DIFFRACTIONf_chiral_restr0.021583
X-RAY DIFFRACTIONf_plane_restr0.003583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.69320.2745710.24091340X-RAY DIFFRACTION43
2.6932-2.96420.3021360.23562486X-RAY DIFFRACTION81
2.9642-3.3930.27131850.21943045X-RAY DIFFRACTION99
3.393-4.27440.19811590.17553113X-RAY DIFFRACTION99
4.2744-46.11210.2261580.18263145X-RAY DIFFRACTION99
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)
16.58982.64762.34159.16794.16395.16250.05210.3663-0.6050.3210.8427-1.3728-0.13291.6121-0.91020.35270.11930.03310.9423-0.02580.546912.25921.82855.1768
28.09751.8256-1.99945.32550.88817.5566-0.3311.02830.7628-0.9420.23250.6811-1.0384-0.57730.37140.593-0.043-0.04820.37590.08690.3798-7.72996.997540.602
38.00070.24471.61456.1396-0.57577.9256-0.650.9684-0.7253-0.28810.36710.36120.8784-0.52220.25610.4926-0.11950.07460.3928-0.06810.2034-8.8591-0.125144.4421
44.1525-0.85280.89396.0967-0.47412.8294-0.2273-0.1764-0.5873-0.9094-0.182-0.58831.22560.30580.30290.6822-0.01380.18420.2980.06090.3228-4.51-2.750654.7778
55.96262.4501-1.22668.58434.13253.0942-0.01641.35740.9597-0.79660.19890.1384-0.8559-0.414-0.16510.8480.24130.00140.47260.20310.3599-10.211416.139945.9496
60.1270.9190.36098.2032-0.40956.9411-0.05460.3881-0.1105-0.27460.60951.7385-0.6954-1.4559-0.53190.76580.3338-0.05141.16960.36030.8816-23.169813.568550.3494
76.023-1.31421.04397.28460.61476.7508-0.0561-0.0723-0.13730.1669-0.05490.0325-0.35430.03010.10150.25440.02060.05820.27540.01740.1358-5.19317.705959.0045
85.29061.0151-0.14573.90880.13236.4038-0.1124-0.3622-0.09920.1683-0.101-0.3696-0.08990.58250.15960.2248-0.05890.05560.35110.06110.2365-0.31795.946965.0908
93.1074-2.58361.26425.92650.5062.4651-0.03080.1382-1.7905-0.1430.3554-0.19421.0933-1.1571-0.42440.9035-0.44010.0420.6488-0.01440.8726-17.1551-6.97950.198
100.2728-0.3225-0.05470.7706-0.16030.1416-0.11270.31220.2549-0.18680.4853-0.6399-0.63040.92961.11690.5571-0.744-0.2490.932-0.4520.1692-5.629916.844987.275
117.99350.3435-0.48376.1977-0.85575.81720.0008-0.4886-0.32370.3854-0.03680.470.4928-0.6262-0.05310.257-0.03260.00760.27860.00640.1922-24.61310.467984.6153
125.517-1.0422-0.59516.32110.91065.4850.0909-0.0530.6028-0.0687-0.02170.002-0.7722-0.165-0.02680.17680.00130.03840.22730.04340.2396-18.03739.945877.0124
133.447-3.2049-0.92863.06251.44864.5739-0.7128-0.4592-1.06280.0761-0.3613-0.54041.77060.66150.59340.70970.11920.31270.35970.26420.6325-16.0283-10.364684.9521
141.2991-1.32610.17233.0165-2.47613.204-0.02730.23940.4405-0.47520.56660.5339-0.4911-0.0874-0.42431.5539-0.40590.26530.486-0.14931.1848-24.3197-14.814273.6903
155.61671.47943.43822.751-0.19988.1676-0.49080.9487-0.7181-0.7867-0.1036-0.43111.28581.14030.38280.60710.14310.16080.32530.04270.4972-9.8684-8.413274.717
166.87680.8009-0.28992.18741.88861.81720.1829-0.12890.68470.1189-0.2844-0.2337-0.74611.22010.2060.2698-0.1873-0.00930.5384-0.01230.3138-4.530211.079977.7072
175.7057-0.2957-1.52013.3041-0.813.388-0.15610.0381-0.2904-0.3639-0.0560.34580.4037-0.1720.16050.2454-0.0203-0.05510.3465-0.00460.1633-15.41411.964671.2504
180.5375-0.04640.00322.67441.47010.812-0.10990.0445-0.46940.4668-0.15840.39680.3583-0.09810.37981.93080.2109-0.07120.493-0.25120.82-6.0133-14.727847.8078
193.4319-2.85121.37083.98610.63382.4979-0.4846-0.32540.4582-0.0249-0.18650.1186-0.1587-0.3480.17630.75130.45170.39010.71530.28611.2395-29.227616.730280.6111
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 308:322 )A308 - 322
2X-RAY DIFFRACTION2( CHAIN A AND RESID 323:339 )A323 - 339
3X-RAY DIFFRACTION3( CHAIN A AND RESID 340:363 )A340 - 363
4X-RAY DIFFRACTION4( CHAIN A AND RESID 364:394 )A364 - 394
5X-RAY DIFFRACTION5( CHAIN A AND RESID 395:411 )A395 - 411
6X-RAY DIFFRACTION6( CHAIN A AND RESID 412:421 )A412 - 421
7X-RAY DIFFRACTION7( CHAIN A AND RESID 422:468 )A422 - 468
8X-RAY DIFFRACTION8( CHAIN A AND RESID 469:524 )A469 - 524
9X-RAY DIFFRACTION9( CHAIN A AND RESID 525:548 )A525 - 548
10X-RAY DIFFRACTION10( CHAIN B AND RESID 306:322 )B306 - 322
11X-RAY DIFFRACTION11( CHAIN B AND RESID 323:363 )B323 - 363
12X-RAY DIFFRACTION12( CHAIN B AND RESID 364:394 )B364 - 394
13X-RAY DIFFRACTION13( CHAIN B AND RESID 395:411 )B395 - 411
14X-RAY DIFFRACTION14( CHAIN B AND RESID 412:421 )B412 - 421
15X-RAY DIFFRACTION15( CHAIN B AND RESID 422:438 )B422 - 438
16X-RAY DIFFRACTION16( CHAIN B AND RESID 439:496 )B439 - 496
17X-RAY DIFFRACTION17( CHAIN B AND RESID 497:548 )B497 - 548
18X-RAY DIFFRACTION18( CHAIN C AND RESID 688:695 )C688 - 695
19X-RAY DIFFRACTION19( CHAIN D AND RESID 688:696 )D688 - 696

+
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