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- EMDB-6241: The Structure of a Biologically Active Estrogen Receptor-Coactiva... -

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Basic information

Entry
Database: EMDB / ID: EMD-6241
TitleThe Structure of a Biologically Active Estrogen Receptor-Coactivator Complex on DNA
Map dataERa/SRC-3/p300 complex
Sample
  • Sample: ERa/SRC-3/p300 complex
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: p300
KeywordsEstrogen receptor
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
DepositionJan 14, 2015-
Header (metadata) releaseJan 28, 2015-
Map releaseApr 13, 2016-
UpdateApr 27, 2016-
Current statusApr 27, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6241.gif

Downloads & links

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Map

FileDownload / File: emd_6241.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationERa/SRC-3/p300 complex
Voxel sizeX=Y=Z: 2.16 Å
Density
Contour LevelBy EMDB: 1.0 / Movie #1: 0.5
Minimum - Maximum-0.00729616 - 3.63913774
Average (Standard dev.)0.04936328 (±0.22845118)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
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-100-100-100
NC/NR/NS200200200
D min/max/mean-0.0073.6390.049

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Supplemental data

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Supplemental map: ER ab1.map

FileER_ab1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: ER af1ab.map

FileER_af1ab.map
Projections & Slices
AxesZYX

Projections

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Histogram

Histogram (log scale)

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Supplemental map: p300-ab1.map

Filep300-ab1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: p300-ab2.map

Filep300-ab2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Supplemental map: p300.map

Filep300.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ERa/SRC-3/p300 complex

EntireName: ERa/SRC-3/p300 complex
Components
  • Sample: ERa/SRC-3/p300 complex
  • Protein or peptide: estrogen receptor alpha
  • Protein or peptide: steroid receptor coactivator-3
  • Protein or peptide: p300

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Supramolecule #1000: ERa/SRC-3/p300 complex

SupramoleculeName: ERa/SRC-3/p300 complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 800 KDa / Theoretical: 770 KDa / Method: Sedimentation

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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)

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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)

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Macromolecule #3: p300

MacromoleculeName: p300 / type: protein_or_peptide / ID: 3 / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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

BufferpH: 7.5
GridDetails: continuous carbon film supported by a 200-mesh R1.2/1.3 Quantifoil grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot 1 second prior to plunging.

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
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) / Digitization - Sampling interval: 15 µm / Number real images: 806 / Average electron dose: 25 e/Å2

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Image processing

CTF correctionDetails: per image
Final angle assignmentDetails: EMAN2: final search angle 2 degrees
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 18120
DetailsRefinements were carried out with a final search angle of 2 degrees using the e2refine.py program.

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