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- EMDB-10630: Interaction of the CoREST complex with a nucleosome with 185 bp 6... -

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Basic information

Entry
Database: EMDB / ID: EMD-10630
TitleInteraction of the CoREST complex with a nucleosome with 185 bp 601 sequence DNA and a propargylamine mimic of dimethy Lys4 histone H3
Map data
Sample
  • Complex: Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1)
KeywordsCoREST / RCOR1 / HDAC1 / LSD1 / nucleosome / GENE REGULATION
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 26.1 Å
AuthorsSong Y / Fairall L / Wu M / Ragan TJ / Savva CG / Morone N / Cole PA / 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-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10630.png

Downloads & links

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Map

FileDownload / File: emd_10630.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.)
1.83 Å/pix.
x 200 pix.
= 366. Å		1.83 Å/pix.
x 200 pix.
= 366. Å		1.83 Å/pix.
x 200 pix.
= 366. Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.016
Minimum - Maximum-0.0069275475 - 0.061211452
Average (Standard dev.)0.00045274908 (±0.0042518177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 366.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.831.831.83
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z366.000366.000366.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0070.0610.000

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Supplemental data

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Half map: #1

Fileemd_10630_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10630_half_map_2.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 : Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1)

EntireName: Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1)
Components
  • Complex: Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1)

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Supramolecule #1: Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1)

SupramoleculeName: Nucleosome with CoREST complex (RCOR1: LSD1:HDAC1) / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 410 KDa

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Experimental details

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Structure determination

Methodnegative staining
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
StainingType: NEGATIVE / Material: uranyl acetate
GridModel: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
DetailsSample was crosslinked with 0.01% glutaraldehyde

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-48 / Number grids imaged: 1 / Number real images: 384 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Particle selectionNumber selected: 23126
Startup modelType of model: INSILICO MODEL / In silico model: Relion 3.0 Initial Model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 5204
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3)
Final 3D classificationSoftware - Name: RELION (ver. 3)

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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

1aoi

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

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