[English] 日本語
Yorodumi
- EMDB-6264: ERE-DNA/ERalpha/SRC-3/p300 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6264
TitleERE-DNA/ERalpha/SRC-3/p300 complex
Map dataERE-DNA/ERalpha/SRC-3/p300 complex
Sample
  • Sample: ERE-DNA/ERalpha/SRC-3/p300 complex
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: histone acetyltransferase p300
  • DNA: estrogen response element
KeywordsEstrogen Receptor
Function / homologytranscription regulator complex
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsYi P / Wang Z / Feng Q / Pintilie GD / Foulds CE / Lanz RB / Ludtke SJ / Schmid MF / Chiu W / O'Malley BW
CitationJournal: Mol Cell / Year: 2015
Title: Structure of a biologically active estrogen receptor-coactivator complex on DNA.
Authors: Ping Yi / Zhao Wang / Qin Feng / Grigore D Pintilie / Charles E Foulds / Rainer B Lanz / Steven J Ludtke / Michael F Schmid / Wah Chiu / Bert W O'Malley /
Abstract: Estrogen receptor (ER/ESR1) is a transcription factor critical for development, reproduction, metabolism, and cancer. ER function hinges on its ability to recruit primary and secondary coactivators, ...Estrogen receptor (ER/ESR1) is a transcription factor critical for development, reproduction, metabolism, and cancer. ER function hinges on its ability to recruit primary and secondary coactivators, yet structural information on the full-length receptor-coactivator complex to complement preexisting and sometimes controversial biochemical information is lacking. Here, we use cryoelectron microscopy (cryo-EM) to determine the quaternary structure of an active complex of DNA-bound ERα, steroid receptor coactivator 3 (SRC-3/NCOA3), and a secondary coactivator (p300/EP300). Our structural model suggests the following assembly mechanism for the complex: each of the two ligand-bound ERα monomers independently recruits one SRC-3 protein via the transactivation domain of ERα; the two SRC-3s in turn bind to different regions of one p300 protein through multiple contacts. We also present structural evidence for the location of activation function 1 (AF-1) in a full-length nuclear receptor, which supports a role for AF-1 in SRC-3 recruitment.
History
DepositionFeb 2, 2015-
Header (metadata) releaseMar 18, 2015-
Map releaseAug 26, 2015-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.340081359
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.340081359
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6264.gif

Downloads & links

-
Map

FileDownload / File: emd_6264.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationERE-DNA/ERalpha/SRC-3/p300 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 200 pix.
= 432. Å		2.16 Å/pix.
x 200 pix.
= 432. Å		2.16 Å/pix.
x 200 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 1.5 / Movie #1: 2.3400814
Minimum - Maximum-0.03193748 - 15.929608350000001
Average (Standard dev.)0.21607803 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-98
Dimensions200200200
Spacing200200200
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.162.162.16
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-98
NC/NR/NS200200200
D min/max/mean-0.03215.9300.216

-
Supplemental data

-
Sample components

-
Entire : ERE-DNA/ERalpha/SRC-3/p300 complex

EntireName: ERE-DNA/ERalpha/SRC-3/p300 complex
Components
  • Sample: ERE-DNA/ERalpha/SRC-3/p300 complex
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: histone acetyltransferase p300
  • DNA: estrogen response element

-
Supramolecule #1000: ERE-DNA/ERalpha/SRC-3/p300 complex

SupramoleculeName: ERE-DNA/ERalpha/SRC-3/p300 complex / type: sample / ID: 1000 / Number unique components: 4
Molecular weightExperimental: 770 KDa / Theoretical: 800 KDa

-
Macromolecule #1: estrogen receptor alpha

MacromoleculeName: estrogen receptor alpha / type: protein_or_peptide / ID: 1 / Name.synonym: ERalpha / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9
SequenceGO: transcription regulator complex

-
Macromolecule #2: steroid receptor coactivator-3

MacromoleculeName: steroid receptor coactivator-3 / type: protein_or_peptide / ID: 2 / Name.synonym: SRC-3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9
SequenceGO: transcription regulator complex

-
Macromolecule #3: histone acetyltransferase p300

MacromoleculeName: histone acetyltransferase p300 / type: protein_or_peptide / ID: 3 / Name.synonym: EP300 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: SF9
SequenceGO: transcription regulator complex

-
Macromolecule #4: estrogen response element

MacromoleculeName: estrogen response element / type: dna / ID: 4 / Name.synonym: ERE DNA / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Details: 100 mM Tris-HCl, 50 mM NaCl, 10 mM MgCl2, 0.025% Triton X-100, 1mM DTT
GridDetails: 200 mesh gold grid with thin carbon support
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1-2 seconds before plunging.

-
Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 90 K / Max: 105 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateOct 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 806 / Average electron dose: 25 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: 60 degree holder / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsEMAN2 and Relion 1.3
CTF correctionDetails: per frame
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 18120

+
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