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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ppp
TitleCrystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with Fluoro-Resveratrol
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 / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / 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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / 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 / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone mediated signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / protein localization to chromatin / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / Regulation of lipid metabolism by PPARalpha / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / nitric-oxide synthase regulator activity / ESR-mediated signaling / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / negative regulation of miRNA transcription / response to progesterone / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / nuclear receptor binding / positive regulation of nitric-oxide synthase activity / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / male gonad development / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / HATs acetylate histones / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Retinoid X Receptor / Retinoid X Receptor / 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-FSV / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.686 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)58,4356
Polymers57,9424
Non-polymers4922
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-33 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.190, 81.930, 58.470
Angle α, β, γ (deg.)90.00, 110.86, 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: 1138.383 Da / Num. of mol.: 2
Fragment: receptor-interacting peptide (UNP residues 688-696)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-FSV / 5-[(E)-2-(3-fluoro-4-hydroxyphenyl)ethenyl]benzene-1,3-diol / fluoro-resveratrol


Mass: 246.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11FO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.09 Å3/Da / Density % sol: 41.24 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationMonochromator: Side scattering bent cube i-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.684→46.3 Å / Num. all: 11884 / Num. obs: 11884 / % possible obs: 88.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 22.5
Reflection shellResolution: 2.684→2.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / Num. unique all: 481 / % possible all: 35.98

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QA8

2qa8


Resolution: 2.686→46.247 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 1148 10.04 %RANDOM
Rwork0.2 ---
all0.2048 11884 --
obs0.2048 11433 85.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.686→46.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 36 42 3780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023833
X-RAY DIFFRACTIONf_angle_d0.565193
X-RAY DIFFRACTIONf_dihedral_angle_d14.0341373
X-RAY DIFFRACTIONf_chiral_restr0.022618
X-RAY DIFFRACTIONf_plane_restr0.002642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.686-2.80820.3474570.2749553X-RAY DIFFRACTION36
2.8082-2.95630.30631200.25311024X-RAY DIFFRACTION70
2.9563-3.14150.31221650.23821380X-RAY DIFFRACTION92
3.1415-3.38390.31761570.22791427X-RAY DIFFRACTION95
3.3839-3.72440.24191590.20341452X-RAY DIFFRACTION96
3.7244-4.26290.2361590.17931441X-RAY DIFFRACTION95
4.2629-5.36960.23451640.16941503X-RAY DIFFRACTION99
5.3696-46.25370.1981670.19451505X-RAY DIFFRACTION98
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)
17.5174-1.0589-1.60423.99441.75275.44130.18990.80780.2762-0.4369-0.2168-0.3923-0.3466-0.30430.0290.382-0.00620.01440.33550.06510.241913.71437.625-3.0988
26.2395-1.2627-2.56646.59240.29357.0547-0.3720.3397-0.68160.56680.0539-0.24331.1683-0.06810.18860.38530.02960.02450.2641-0.04360.257612.8438-2.58844.4396
37.30720.6962-2.41044.23171.11876.79420.00940.15490.19270.1476-0.1261-0.12250.0121-0.17130.08730.23580.0377-0.04760.3085-0.0080.1226.66516.13187.6314
45.5421-0.4866-0.55434.07670.178410.7153-0.2639-0.38810.05180.42740.0783-0.08370.0630.27930.11120.34880.00560.04610.2831-0.07450.21192.20056.275631.4793
51.9295-1.37950.6552.595-0.29960.26060.69151.1380.6369-0.1618-0.5771-0.2022-0.05590.4885-0.15231.57220.07610.49731.04520.07480.7372-0.4-12.965414.6022
63.9594-0.3377-1.11874.16450.31927.3655-0.1777-0.1921-0.27380.2774-0.0804-0.0590.7533-0.09490.11470.33710.01850.05950.3403-0.03640.26271.13653.20121.6809
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 305:369)
2X-RAY DIFFRACTION2(chain A and resid 370:435)
3X-RAY DIFFRACTION3(chain A and resid 436:548)
4X-RAY DIFFRACTION4(chain B and resid 309:458)
5X-RAY DIFFRACTION5(chain B and resid 459:469)
6X-RAY DIFFRACTION6(chain B and resid 470:548)

+
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