[English] 日本語
Yorodumi
- PDB-5ehj: Crystal Structure of the ER-alpha Ligand-binding Domain in Comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ehj
TitleCrystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol
Components
  • Estrogen receptor
  • NCOA2
KeywordsTRANSCRIPTION / Nuclear receptor / transcription factor / ligand binding / protein-ligand complex
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid 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 / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific
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 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 / 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
Chem-5K5 / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. ...Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Cavett, V. / Nowak, J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
CitationJournal: Mol.Syst.Biol. / Year: 2016
Title: Predictive features of ligand-specific signaling through the estrogen receptor.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Zheng, Y. / Wang, S. / Min, J. / Dong, C. / Liao, Z. / Nowak, J. / Wright, N.J. / Houtman, R. / Carlson, K.E. / Josan, J.S. / Elemento, O. / Katzenellenbogen, J.A. / Zhou, H.B. / Nettles, K.W.
History
DepositionOct 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
C: NCOA2
D: NCOA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6026
Polymers61,9334
Non-polymers6692
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-30 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.000, 81.990, 58.320
Angle α, β, γ (deg.)90.000, 110.450, 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: 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) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Protein/peptide NCOA2


Mass: 1666.943 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-5K5 / 4,4'-[(4aR,8aR)-octahydronaphthalen-2(1H)-ylidenemethanediyl]diphenol


Mass: 334.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 15% PEG 3350, 0.05M MgCl2, 0.067M NaCl, 0.1M Tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2012
RadiationMonochromator: Side scattering bent cube i-beam single crystal asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 16733 / % possible obs: 98.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 29.78 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.133 / Χ2: 0.911 / Net I/av σ(I): 16.337 / Net I/σ(I): 4.9 / Num. measured all: 113908
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.5-2.546.98090.7440.4130.49398.7
2.54-2.596.98560.8250.3370.47499.10.830.897
2.59-2.646.88230.8940.2950.49598.30.720.779
2.64-2.696.78350.8850.2650.58198.60.6380.693
2.69-2.756.58450.9210.2180.52798.30.5180.563
2.75-2.825.87860.9280.2030.53394.50.4540.499
2.82-2.896.68230.9340.1720.56698.60.4120.448
2.89-2.967.28460.9670.1240.60499.40.310.334
2.96-3.057.18580.9770.1080.60699.80.2690.29
3.05-3.157.18190.9790.0950.69599.90.2380.257
3.15-3.267.18710.9830.0820.72599.70.2040.22
3.26-3.3978340.9890.0660.81199.60.1630.176
3.39-3.5578300.9840.0610.99398.90.1490.162
3.55-3.736.98450.990.0531.16198.30.1280.139
3.73-3.976.68270.9920.0461.299980.110.12
3.97-4.276.28150.9920.0431.35294.90.0990.108
4.27-4.77.28440.9920.0391.41499.40.0960.103
4.7-5.387.18500.9930.0381.47299.10.0940.101
5.38-6.786.88510.9910.0411.268990.0980.106
6.78-506.68660.9980.0282.10897.30.0670.073

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.459 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1532 10.05 %
Rwork0.2092 13716 -
obs0.2137 15248 89.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.25 Å2 / Biso mean: 41.6753 Å2 / Biso min: 2.35 Å2
Refinement stepCycle: final / Resolution: 2.5→46.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3700 0 50 108 3858
Biso mean--35.82 34.38 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023819
X-RAY DIFFRACTIONf_angle_d0.5395178
X-RAY DIFFRACTIONf_chiral_restr0.02625
X-RAY DIFFRACTIONf_plane_restr0.002639
X-RAY DIFFRACTIONf_dihedral_angle_d11.5461370
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4936-2.5740.3275900.267285994962
2.574-2.6660.37251330.25671157129084
2.666-2.77280.26131240.25481176130084
2.7728-2.89890.28991410.25651189133086
2.8989-3.05170.2771500.24081296144694
3.0517-3.24290.30961480.24181326147495
3.2429-3.49320.27681470.22531288143595
3.4932-3.84460.25081490.19541324147395
3.8446-4.40060.2141500.1741325147595
4.4006-5.54280.22151520.17171391154399
5.5428-46.46720.20741480.19271385153397
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)
15.6702-3.7193-1.48098.19670.8592.65070.56710.8230.5852-0.9395-0.6296-0.5731-0.0351-0.2710.22270.24-0.0356-0.01950.35210.01590.1284-5.462120.1924-33.0609
23.6636-0.0298-0.6162.31961.13943.5938-0.14320.0882-0.18860.1271-0.1103-0.10110.36010.04360.21040.23580.00850.04370.18730.01270.1622-2.654915.9636-24.9404
34.7876-0.6672-0.50871.91970.58692.71380.02690.0270.0398-0.0542-0.0505-0.06750.1236-0.02110.06590.23150.02190.01120.17920.02280.1218-9.977121.8032-19.8549
46.0113-0.28122.73895.18071.8135.47870.0356-0.13130.4490.59330.90931.40920.0882-1.47820.03750.0953-0.1709-0.06450.61920.15730.4277-34.002315.7144-2.5772
54.3275-0.08790.75994.50111.14686.6163-0.1471-0.7437-0.25860.33180.1266-0.2740.19530.30220.07090.23950.08320.05480.24950.02460.2071-11.53919.149612.4783
63.0227-0.2476-0.46052.7182-0.18664.1463-0.0995-0.2941-0.3953-0.0742-0.1457-0.10850.23210.0390.17890.23350.01340.02140.20040.00410.1081-15.383516.97371.4401
76.0899-2.4216-5.14852.8699-0.49677.3919-0.1492-0.02770.35410.46571.2742-1.6726-1.9761.562-0.33750.2998-0.171-0.13620.7451-0.34480.4561-3.314530.35719.3579
82.99080.02060.95424.13750.91364.0454-0.05830.20310.1789-0.2107-0.0474-0.1409-0.6554-0.09780.0830.2209-0.00660.02950.27510.01110.1654-15.655326.907-2.9812
92.647-3.8441-1.43629.17161.47210.904-0.51390.3098-0.5557-1.4057-0.07281.14160.01620.61530.62481.2298-0.18050.0630.61-0.10210.4532-18.28863.2157-12.4554
104.2022-1.65570.24482.8201-0.42133.6029-0.1225-0.04710.1508-0.1016-0.0322-0.0257-0.1419-0.31340.14640.1781-0.00620.03960.2161-0.03160.1224-17.976421.8004-8.5507
116.50851.9375-1.54954.68320.01574.530.3544-0.56450.3634-0.4925-0.3821-1.86360.09340.9592-0.02960.55140.121-0.01310.40550.11190.7195-2.74228.62446.4207
128.9034-2.2991.96383.7881-1.48742.6014-0.1255-1.379-2.4454-0.2412-0.053-0.2431-0.011-0.48130.23130.5662-0.06740.04890.37170.19530.478-15.66121.00777.9462
134.7279-1.05421.54085.26832.77975.44841.0668-0.06870.7585-0.5722-0.1825-0.0737-0.91250.4254-0.3480.2728-0.07040.20550.37870.03760.52989.067932.5236-25.7319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 305 through 338 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 339 through 437 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 548 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 305 through 320 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 321 through 363 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 405 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 406 through 420 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 421 through 455 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 456 through 473 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 474 through 531 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 532 through 548 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 688 through 696 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 687 through 696 )D0

+
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