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- EMDB-17158: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17158
TitleCryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (constituent map 2 from additional focus classification on PAS domains)
Map dataFull map.
Sample
  • Complex: CLOCK-BMAL1 bound to a nucleosome SHL+5.8
    • Complex: Nucleosomal core particle
      • Complex: Histone octamer
      • Complex: Nucleosomal DNA
    • Complex: CLOCK-BMAL1 heterodimer
KeywordsE-box / transcription factor / circadian clock / GENE REGULATION
Biological speciesHomo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsStoos L / Michael AK / Kempf G / Cavadini S / Thoma NH
Funding supportEuropean Union, France, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)884331European Union
Human Frontier Science Program (HFSP)LT000646/2018-L5 France
CitationJournal: Nature / Year: 2023
Title: Cooperation between bHLH transcription factors and histones for DNA access.
Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas ...Authors: Alicia K Michael / Lisa Stoos / Priya Crosby / Nikolas Eggers / Xinyu Y Nie / Kristina Makasheva / Martina Minnich / Kelly L Healy / Joscha Weiss / Georg Kempf / Simone Cavadini / Lukas Kater / Jan Seebacher / Luca Vecchia / Deyasini Chakraborty / Luke Isbel / Ralph S Grand / Florian Andersch / Jennifer L Fribourgh / Dirk Schübeler / Johannes Zuber / Andrew C Liu / Peter B Becker / Beat Fierz / Carrie L Partch / Jerome S Menet / Nicolas H Thomä /
Abstract: The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged ...The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members. Here we investigate how chromatinized E-boxes are engaged by two structurally diverse bHLH proteins: the proto-oncogene MYC-MAX and the circadian transcription factor CLOCK-BMAL1 (refs. ). Both transcription factors bind to E-boxes preferentially near the nucleosomal entry-exit sites. Structural studies with engineered or native nucleosome sequences show that MYC-MAX or CLOCK-BMAL1 triggers the release of DNA from histones to gain access. Atop the H2A-H2B acidic patch, the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes at endogenous DNA sequences occurs through direct interactions between two CLOCK-BMAL1 protomers and histones and is important for circadian cycling. At internal E-boxes, the MYC-MAX leucine zipper can also interact with histones H2B and H3, and its binding is indirectly enhanced by OCT4 elsewhere on the nucleosome. The nucleosomal E-box position and the type of bHLH dimerization domain jointly determine the histone contact, the affinity and the degree of competition and cooperativity with other nucleosome-bound factors.
History
DepositionApr 19, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17158.png

Downloads & links

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Map

FileDownload / File: emd_17158.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00346
Minimum - Maximum-0.0080509875 - 0.025184222
Average (Standard dev.)-0.0000125065135 (±0.0009029907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A.

Fileemd_17158_half_map_1.map
AnnotationHalf-map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B.

Fileemd_17158_half_map_2.map
AnnotationHalf-map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CLOCK-BMAL1 bound to a nucleosome SHL+5.8

EntireName: CLOCK-BMAL1 bound to a nucleosome SHL+5.8
Components
  • Complex: CLOCK-BMAL1 bound to a nucleosome SHL+5.8
    • Complex: Nucleosomal core particle
      • Complex: Histone octamer
      • Complex: Nucleosomal DNA
    • Complex: CLOCK-BMAL1 heterodimer

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Supramolecule #1: CLOCK-BMAL1 bound to a nucleosome SHL+5.8

SupramoleculeName: CLOCK-BMAL1 bound to a nucleosome SHL+5.8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Nucleosomal core particle

SupramoleculeName: Nucleosomal core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Histone octamer

SupramoleculeName: Histone octamer / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Nucleosomal DNA

SupramoleculeName: Nucleosomal DNA / type: complex / ID: 4 / Parent: 2 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Supramolecule #5: CLOCK-BMAL1 heterodimer

SupramoleculeName: CLOCK-BMAL1 heterodimer / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13350
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4h10

source_name: PDB, initial_model_type: experimental model

4f3l

source_name: PDB, initial_model_type: experimental model

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