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- EMDB-10629: Cryo EM map of BS3 crosslinked CoREST complex (LSD1:RCOR1:HDAC1) ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-10629
TitleCryo EM map of BS3 crosslinked CoREST complex (LSD1:RCOR1:HDAC1) - open form
Map data
Sample
  • Complex: Ternary complex of RCOR1 with the demethylase LSD1 and the deacetylase HDAC1
KeywordsCoREST / RCOR1 / HDAC1 / LSD1 / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 21.5 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-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10629.png

Downloads & links

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Map

FileDownload / File: emd_10629.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.007937333 - 0.029882746
Average (Standard dev.)0.00017250027 (±0.0018968353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z280.000280.000280.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0080.0300.000

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Supplemental data

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Half map: #2

Fileemd_10629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10629_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)
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
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 2mM BS3 at room temperature for 5 minutes

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K
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 - Frames/image: 1-36 / Number grids imaged: 1 / Number real images: 1885 / Average exposure time: 14.0 sec. / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 164247 / Details: Particles picked using crYOLO
Startup modelType of model: INSILICO MODEL / In silico model: Relion 3.0 Initial Model
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 6825

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Atomic model buiding 1

Initial model
PDB IDChain

1bkx

source_name: PDB, initial_model_type: experimental model

2vid

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT

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