[English] 日本語
Yorodumi
- PDB-4pps: Crystal Structure of the Estrogen Receptor alpha Ligand-binding D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pps
TitleCrystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with an A-CD ring estrogen derivative
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsPROTEIN BINDING / nuclear hormone receptor / transcription factor / ligand-binding / nucleus
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / 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 / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway ...regulation of epithelial cell apoptotic process / 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 / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / locomotor rhythm / mammary gland branching involved in pregnancy / uterus development / negative regulation of smooth muscle cell apoptotic process / aryl hydrocarbon receptor binding / vagina development / TFIIB-class transcription factor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / androgen metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / 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 receptor-mediated steroid hormone signaling pathway / negative regulation of DNA-binding transcription factor activity / positive regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / cellular response to hormone stimulus / Recycling of bile acids and salts / RNA polymerase II preinitiation complex assembly / transcription regulator inhibitor activity / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / : / positive regulation of adipose tissue development / steroid binding / 14-3-3 protein binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / 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 / negative regulation of smoothened signaling pathway / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / euchromatin / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / response to estrogen / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / : / response to estradiol / PIP3 activates AKT signaling / HATs acetylate histones / positive regulation of cytosolic calcium ion concentration / 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 / 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
Chem-ESE / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsNwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
CitationJournal: Elife / Year: 2014
Title: Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network.
Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)59,0606
Polymers58,5674
Non-polymers4932
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-29 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.106, 84.191, 58.480
Angle α, β, γ (deg.)90.00, 108.35, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 27832.783 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 305-548) / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, 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: 1450.686 Da / Num. of mol.: 2
Fragment: receptor-interacting peptide (UNP residues 687-698)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-ESE / (1S,3aR,5R,7aS)-5-(4-hydroxyphenyl)-7a-methyloctahydro-1H-inden-1-ol


Mass: 246.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H22O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 15% PEG3350, 0.05 M magnesium chloride, 0.067 M sodium chloride, 0.1 M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.929→33.541 Å / Num. all: 38369 / Num. obs: 38369 / % possible obs: 98.68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.7
Reflection shellResolution: 1.929→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3443 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QA8

2qa8


Resolution: 1.929→33.541 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 21.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1883 5.2 %RANDOM
Rwork0.1766 ---
all0.1779 38369 --
obs0.1779 36236 93.22 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.511 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1438 Å20 Å26.6831 Å2
2--2.76 Å2-0 Å2
3----3.9038 Å2
Refinement stepCycle: LAST / Resolution: 1.929→33.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 36 323 4296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024140
X-RAY DIFFRACTIONf_angle_d0.6145614
X-RAY DIFFRACTIONf_dihedral_angle_d12.9081555
X-RAY DIFFRACTIONf_chiral_restr0.044659
X-RAY DIFFRACTIONf_plane_restr0.002699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.98160.27951060.24192060X-RAY DIFFRACTION73
1.9816-2.03990.23591170.21182350X-RAY DIFFRACTION84
2.0399-2.10570.23911450.19052517X-RAY DIFFRACTION89
2.1057-2.1810.21311490.18842628X-RAY DIFFRACTION93
2.181-2.26830.26091360.20952436X-RAY DIFFRACTION87
2.2683-2.37150.20811340.18092676X-RAY DIFFRACTION95
2.3715-2.49650.24151610.17862735X-RAY DIFFRACTION97
2.4965-2.65280.22941530.18012793X-RAY DIFFRACTION98
2.6528-2.85750.23421570.18882763X-RAY DIFFRACTION99
2.8575-3.14490.20471530.17892836X-RAY DIFFRACTION100
3.1449-3.59950.2061520.17282837X-RAY DIFFRACTION100
3.5995-4.53330.15151610.14842851X-RAY DIFFRACTION100
4.5333-33.54590.1791590.17452871X-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)
10.0119-0.01330.02120.0492-0.02720.01810.2951-0.4633-0.39060.1064-0.0620.33850.4493-0.5278-0.00010.3221-0.0540.00690.4540.05120.4316-11.0929-7.109929.4648
20.5111-0.4234-0.12850.36180.07740.02820.2522-0.28980.23280.4467-0.0662-0.2833-0.70050.44020.2710.6632-0.19580.00470.4623-0.08680.271111.5299.548245.76
30.81430.13160.73560.8891-0.67571.21210.0143-0.0846-0.20750.125-0.01590.00260.1584-0.0038-0.01160.2587-0.0099-0.00190.1849-0.00720.21218.1519-4.058433.996
41.1138-0.21690.21280.8677-0.41170.9904-0.2368-0.25020.19250.5013-0.0564-0.3417-0.68370.31-0.17210.4475-0.0744-0.0650.1934-0.03780.247412.664614.755135.5612
50.12890.16890.01470.1922-0.02670.0576-0.0930.15820.533-0.2787-0.0399-0.0856-0.55520.1185-0.00020.3266-0.04410.00310.2427-0.03210.24149.462313.237725.7553
60.27630.14220.34050.14220.08540.3743-0.09460.0752-0.1030.0465-0.01920.30970.0094-0.28830.00010.21470.03230.00470.2322-0.0210.2182-1.84331.743725.5906
71.9478-1.2112.01610.8411-1.23212.46280.2020.0435-0.5463-0.48550.29330.04340.95180.51730.32720.3981-0.0720.04310.6818-0.16160.41848.3568-14.565818.9675
81.00880.3114-0.20950.47960.05241.0696-0.12030.0143-0.4498-0.0334-0.09680.33280.5669-0.3942-0.07560.225-0.02860.00410.2813-0.01680.2718-6.8661-6.324219.2448
90.46070.4172-0.47151.15510.21640.78840.1391-0.03370.30970.0259-0.1529-0.0843-0.0410.14260.00150.1905-0.0318-0.00220.2073-0.02710.18798.94243.743321.3733
100.277-0.42990.14270.8875-0.53051.20170.18290.1897-0.1689-0.0233-0.4456-1.01620.11531.1987-0.05110.4352-0.0342-0.08620.48490.02430.422221.9483-5.237636.0876
110.3846-0.0996-0.41480.955-0.37670.40720.07320.380.2926-0.1801-0.0567-0.319-0.01180.01320.0370.30570.0138-0.0070.22640.00870.204215.62890.1509-4.2167
121.2264-0.045-0.54871.70090.26251.15290.02250.05420.0009-0.1024-0.0217-0.01510.00160.0182-0.00010.1602-0.0086-0.00290.157-0.00870.156118.9483-2.69154.7412
131.6497-0.4607-0.8790.79710.17270.73540.06480.01950.3023-0.0289-0.0111-0.0501-0.0853-0.06390.00270.135-0.0108-0.00640.15770.00490.170410.15382.8879.5667
143.13782.19792.7834.24052.89462.80430.4705-0.7641-0.320.5298-0.20770.81070.7346-0.9701-0.07040.56720.0593-0.02090.32450.08580.24459.6719-16.220239.2206
150.12-0.023-0.06970.01510.03230.1243-0.00890.19530.4527-0.41410.033-0.7075-0.58550.61940.00710.34350.02910.10350.29310.08310.430324.600217.11271.0381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 305:322 )
2X-RAY DIFFRACTION2chain 'A' and (resid 323:338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339:395 )
4X-RAY DIFFRACTION4chain 'A' and (resid 396:421 )
5X-RAY DIFFRACTION5chain 'A' and (resid 422:437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438:455 )
7X-RAY DIFFRACTION7chain 'A' and (resid 456:468 )
8X-RAY DIFFRACTION8chain 'A' and (resid 469:496 )
9X-RAY DIFFRACTION9chain 'A' and (resid 497:530 )
10X-RAY DIFFRACTION10chain 'A' and (resid 531:548 )
11X-RAY DIFFRACTION11chain 'B' and (resid 305:338 )
12X-RAY DIFFRACTION12chain 'B' and (resid 339:438 )
13X-RAY DIFFRACTION13chain 'B' and (resid 439:548 )
14X-RAY DIFFRACTION14chain 'C' and (resid 687:698 )
15X-RAY DIFFRACTION15chain 'D' and (resid 688:696 )

+
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