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- EMDB-17184: MYC-MAX bound to a nucleosome at SHL+5.8 -

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Basic information

Entry
Database: EMDB / ID: EMD-17184
TitleMYC-MAX bound to a nucleosome at SHL+5.8
Map dataMap post-processed with LocScale.
Sample
  • Complex: MYC-MAX bound to a nucleosome at SHL+5.8
    • Complex: Nucleosomal core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1Histone H3
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (144-MER)
        • DNA: DNA (144-MER)
    • Complex: cMYC/MAX heterodimer
      • Protein or peptide: Myc proto-oncogene protein
      • Protein or peptide: Protein max
    • Protein or peptide: Histone H2A type 1-K
  • Ligand: PENTANEDIALGlutaraldehyde
KeywordsE-box / TRANSCRIPTION
Function / homology
Function and homology information


Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / RNA polymerase II transcription repressor complex / Metalloprotease DUBs / regulation of cell cycle process ...Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / Deposition of new CENPA-containing nucleosomes at the centromere / Condensation of Prophase Chromosomes / RNA polymerase II transcription repressor complex / Metalloprotease DUBs / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / UCH proteinases / PRC2 methylates histones and DNA / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / negative regulation of cell division / negative regulation of monocyte differentiation / DNA methylation-dependent heterochromatin formation / Transcription of E2F targets under negative control by DREAM complex / Ub-specific processing proteases / protein-DNA complex disassembly / transcription regulator activator activity / response to growth factor / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / Transcriptional Regulation by E2F6 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / chromosome organization / negative regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Cyclin E associated events during G1/S transition / Packaging Of Telomere Ends / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of telomerase activity / ERK1 and ERK2 cascade / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / positive regulation of epithelial cell proliferation / HDACs deacetylate histones / transcription coregulator binding / protein-DNA complex / response to gamma radiation / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / NOTCH1 Intracellular Domain Regulates Transcription / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Constitutive Signaling by NOTCH1 PEST Domain Mutants
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Myc proto-oncogene protein / Histone H2A type 1-B/E / Histone H2B type 1-J / Protein max / Histone H4 / Histone H3.1 / Histone H2A type 1-K
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsStoos L / Michael AK / Kempf G / Kater L / Cavadini S / Thoma N
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 21, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17184.png

Downloads & links

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Map

FileDownload / File: emd_17184.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap post-processed with LocScale.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 270.4 Å		0.85 Å/pix.
x 320 pix.
= 270.4 Å		0.85 Å/pix.
x 320 pix.
= 270.4 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: 0.0581
Minimum - Maximum-0.21459335 - 0.6874267
Average (Standard dev.)0.0017866855 (±0.018146224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 270.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Full map.

Fileemd_17184_additional_1.map
AnnotationFull map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A.

Fileemd_17184_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_17184_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 : MYC-MAX bound to a nucleosome at SHL+5.8

EntireName: MYC-MAX bound to a nucleosome at SHL+5.8
Components
  • Complex: MYC-MAX bound to a nucleosome at SHL+5.8
    • Complex: Nucleosomal core particle
      • Complex: Histone octamer
        • Protein or peptide: Histone H3.1Histone H3
        • Protein or peptide: Histone H4
        • Protein or peptide: Histone H2A type 1-B/E
        • Protein or peptide: Histone H2B type 1-J
      • Complex: Nucleosomal DNA
        • DNA: DNA (144-MER)
        • DNA: DNA (144-MER)
    • Complex: cMYC/MAX heterodimer
      • Protein or peptide: Myc proto-oncogene protein
      • Protein or peptide: Protein max
    • Protein or peptide: Histone H2A type 1-K
  • Ligand: PENTANEDIALGlutaraldehyde

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Supramolecule #1: MYC-MAX bound to a nucleosome at SHL+5.8

SupramoleculeName: MYC-MAX bound to a nucleosome at SHL+5.8 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9

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Supramolecule #2: Nucleosomal core particle

SupramoleculeName: Nucleosomal core particle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #6-#7

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Supramolecule #3: cMYC/MAX heterodimer

SupramoleculeName: cMYC/MAX heterodimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #8-#9
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Histone octamer

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

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Supramolecule #5: Nucleosomal DNA

SupramoleculeName: Nucleosomal DNA / type: complex / ID: 5 / Parent: 2 / Macromolecule list: #6-#7
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.17909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HRYRPGTVAL REIRRYQKST ELLIRKLPFQ RLVREIAQDF KTDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLA RRIRGE

UniProtKB: Histone H3.1

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.279875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYAL KRQGRTLYGF GG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.896886 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GKARAKAKTR SSRAGLQFPV GRVHRLLRKG NYSERVGAGA PVYLAAVLEY LTAEILELAG NAARDNKKTR IIPRHLQLAI RNDEELNKL LGRVTIAQGG VLPNIQAVLL

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.334827 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SRKESYSIYV YKVLKQVHPD TGISSKAMGI MNSFVNDIFE RIAGEASRLA HYNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTK YTSA

UniProtKB: Histone H2B type 1-J

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Macromolecule #5: Histone H2A type 1-K

MacromoleculeName: Histone H2A type 1-K / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.807769 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLP

UniProtKB: Histone H2A type 1-K

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Macromolecule #8: Myc proto-oncogene protein

MacromoleculeName: Myc proto-oncogene protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.346392 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
NVKRRTHNVL ERQRRNELKR SFFALRDQIP ELENNEKAPK VVILKKATAY ILS

UniProtKB: Myc proto-oncogene protein

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Macromolecule #9: Protein max

MacromoleculeName: Protein max / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.031737 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DKRAHHNALE RKRRDHIKDS FHSLRDSVPS LQGEKASRAQ ILDKATEYIQ Y

UniProtKB: Protein max

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Macromolecule #6: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.225145 KDa
SequenceString: (DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC) (DA)(DG)(DC)(DT)(DC)(DT) ...String:
(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC) (DG)(DG)(DT)(DC)(DT)(DG)(DC)(DA)(DG)(DG) (DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT) (DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA) (DC) (DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC) (DG)(DC)(DA)(DC)(DG)(DT)(DA) (DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC) (DC)(DC)(DC) (DG)(DC)(DG)(DT)(DT)(DT) (DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA) (DG)(DG)(DG)(DG) (DA)(DT)(DT)(DA)(DC) (DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG) (DC)(DA)(DC)(DG) (DG)(DG)(DT)(DC)(DA)(DC)(DG)(DT)(DG)(DC) (DA)(DT)(DA)(DC)(DA)(DT) (DC)(DC)(DT) (DG)

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Macromolecule #7: DNA (144-MER)

MacromoleculeName: DNA (144-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.67443 KDa
SequenceString: (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DA)(DC)(DC) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DG)(DC)(DA)(DC)(DG)(DT)(DG)(DA)(DC)(DC) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC) (DC)

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Macromolecule #10: PENTANEDIAL

MacromoleculeName: PENTANEDIAL / type: ligand / ID: 10 / Number of copies: 8 / Formula: PTD
Molecular weightTheoretical: 100.116 Da
Chemical component information

ChemComp-PTD:
PENTANEDIAL / Glutaraldehyde

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152914
FSC plot (resolution estimation)

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