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- EMDB-6259: ERE-DNA/ERalpha/SRC-3/p300 complex with antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-6259
TitleERE-DNA/ERalpha/SRC-3/p300 complex with antibody
Map dataER complex with antibody
Sample
  • Sample: ERalpha/SRC-3/p300 complex with antibody 1 (to p300)
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: histone acetyltransferase p300
  • Protein or peptide: p300 antibody
KeywordsEstrogen Receptor
Function / homologytranscription regulator complex
Function and homology information
Biological speciesHomo sapiens (human) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 47.0 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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.8
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6259.gif

Downloads & links

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Map

FileDownload / File: emd_6259.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationER complex with antibody
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.83 Å/pix.
x 200 pix.
= 566. Å		2.83 Å/pix.
x 200 pix.
= 566. Å		2.83 Å/pix.
x 200 pix.
= 566. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 3.5 / Movie #1: 4.8
Minimum - Maximum-0.41244939 - 21.49049187
Average (Standard dev.)0.14118171 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 566.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.832.832.83
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z566.000566.000566.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-0.41221.4900.141

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Supplemental data

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Sample components

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Entire : ERalpha/SRC-3/p300 complex with antibody 1 (to p300)

EntireName: ERalpha/SRC-3/p300 complex with antibody 1 (to p300)
Components
  • Sample: ERalpha/SRC-3/p300 complex with antibody 1 (to p300)
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: histone acetyltransferase p300
  • Protein or peptide: p300 antibody

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Supramolecule #1000: ERalpha/SRC-3/p300 complex with antibody 1 (to p300)

SupramoleculeName: ERalpha/SRC-3/p300 complex with antibody 1 (to p300) / type: sample / ID: 1000 / Number unique components: 4
Molecular weightExperimental: 950 KDa / Theoretical: 920 KDa

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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

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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

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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

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Macromolecule #4: p300 antibody

MacromoleculeName: p300 antibody / type: protein_or_peptide / ID: 4 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 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 grid with continuous carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 90 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 1 second before plunging.

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Electron microscopy

MicroscopeJEOL 2200FS
TemperatureMin: 90 K / Max: 105 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification.
DateOct 1, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 177 / 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: 40000
Sample stageSpecimen holder: 60 degree holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsImages were processed using EMAN2
CTF correctionDetails: per frame
Final reconstructionResolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 3088
Final angle assignmentDetails: EMAN2

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