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- EMDB-10627: Cryo-EM map of glutaraldehye cross-linked CoREST complex (LSD1:RC... -

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Basic information

Entry
Database: EMDB / ID: EMD-10627
TitleCryo-EM map of glutaraldehye cross-linked CoREST complex (LSD1:RCOR1:HDAC1)
Map data
Sample
  • Complex: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 17.5 Å
AuthorsSong Y / Fairall L / Ragan TJ / Savva CG / Morone N / Schwabe JWR
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome TrustWT100237 United Kingdom
CitationJournal: Cell Rep / Year: 2020
Title: Mechanism of Crosstalk between the LSD1 Demethylase and HDAC1 Deacetylase in the CoREST Complex.
Authors: Yun Song / Lisbeth Dagil / Louise Fairall / Naomi Robertson / Mingxuan Wu / T J Ragan / Christos G Savva / Almutasem Saleh / Nobuhiro Morone / Micha B A Kunze / Andrew G Jamieson / Philip A ...Authors: Yun Song / Lisbeth Dagil / Louise Fairall / Naomi Robertson / Mingxuan Wu / T J Ragan / Christos G Savva / Almutasem Saleh / Nobuhiro Morone / Micha B A Kunze / Andrew G Jamieson / Philip A Cole / D Flemming Hansen / John W R Schwabe /
Abstract: The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in ...The transcriptional corepressor complex CoREST is one of seven histone deacetylase complexes that regulate the genome through controlling chromatin acetylation. The CoREST complex is unique in containing both histone demethylase and deacetylase enzymes, LSD1 and HDAC1, held together by the RCOR1 scaffold protein. To date, it has been assumed that the enzymes function independently within the complex. Now, we report the assembly of the ternary complex. Using both structural and functional studies, we show that the activity of the two enzymes is closely coupled and that the complex can exist in at least two distinct states with different kinetics. Electron microscopy of the complex reveals a bi-lobed structure with LSD1 and HDAC1 enzymes at opposite ends of the complex. The structure of CoREST in complex with a nucleosome reveals a mode of chromatin engagement that contrasts with previous models.
History
DepositionJan 20, 2020-
Header (metadata) releaseFeb 19, 2020-
Map releaseMar 11, 2020-
UpdateMar 11, 2020-
Current statusMar 11, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10627.png

Downloads & links

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Map

FileDownload / File: emd_10627.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å		1.08 Å/pix.
x 200 pix.
= 216. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.006751737 - 0.02963598
Average (Standard dev.)0.0006381602 (±0.002600874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 216.00002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z216.000216.000216.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0070.0300.001

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Supplemental data

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Half map: #1

Fileemd_10627_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10627_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of RCOR1 with the demethylase LSD1 and the deacet...

EntireName: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1
Components
  • Complex: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1

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Supramolecule #1: Ternary complex of RCOR1 with the demethylase LSD1 and the deacet...

SupramoleculeName: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pcDNA3
Molecular weightTheoretical: 210 KDa

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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

Concentration0.03 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
50.0 mMKClpotassium chloride
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa / Details: 40 mAmp power
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 30 sec waiting time before blotting. Blot time 4 sec, blot force 10..
DetailsSample was crosslinked with glutaraldehyde in 5-25% sucrose gradient and buffer exchanged to HEPES buffer.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Average exposure time: 12.0 sec. / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 2.4 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 67799 / Details: Particles picked using crYOLO
CTF correctionSoftware - Name: RELION (ver. 3)
Startup modelType of model: INSILICO MODEL / In silico model: Relion 3.0 Initial Model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 17.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 4048
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial model(PDB ID:

1bkx

,

2vid

)
RefinementProtocol: RIGID BODY FIT

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