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Open data
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Basic information
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Title | MYC-MAX bound to a nucleosome at SHL+5.8 | |||||||||
![]() | Map post-processed with LocScale. | |||||||||
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![]() | E-box / TRANSCRIPTION | |||||||||
Function / homology | ![]() Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / Condensation of Prophase Chromosomes / Metalloprotease DUBs / regulation of cell cycle process ...Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / Condensation of Prophase Chromosomes / Metalloprotease DUBs / regulation of cell cycle process / regulation of somatic stem cell population maintenance / PRC2 methylates histones and DNA / Binding of TCF/LEF:CTNNB1 to target gene promoters / UCH proteinases / 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 / Ub-specific processing proteases / transcription regulator activator activity / response to growth factor / Transcription of E2F targets under negative control by DREAM complex / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / regulation of telomere maintenance / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / Transcriptional Regulation by E2F6 / E-box binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / : / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / MLL1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / chromosome organization / 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 / Cyclin E associated events during G1/S transition / Packaging Of Telomere Ends / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / nucleosomal DNA binding / Deposition of new CENPA-containing nucleosomes at the centromere / 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 / ERK1 and ERK2 cascade / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / positive regulation of epithelial cell proliferation / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / transcription coregulator binding / HDACs deacetylate histones / protein-DNA complex / response to gamma radiation / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Formation of the beta-catenin:TCF transactivating complex / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / heterochromatin formation / DNA Damage/Telomere Stress Induced Senescence / NOTCH1 Intracellular Domain Regulates Transcription / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / DNA-binding transcription repressor activity, RNA polymerase II-specific Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Stoos L / Michael AK / Kempf G / Kater L / Cavadini S / Thoma N | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 61.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.3 KB 29.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 110.6 KB | ||
Others | ![]() ![]() ![]() | 62.2 MB 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ottMC ![]() 8osjC ![]() 8oskC ![]() 8oslC ![]() 8otsC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Map post-processed with LocScale. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.845 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Full map.
File | emd_17184_additional_1.map | ||||||||||||
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Annotation | Full map. | ||||||||||||
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Density Histograms |
-Half map: Half-map A.
File | emd_17184_half_map_1.map | ||||||||||||
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Annotation | Half-map A. | ||||||||||||
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Density Histograms |
-Half map: Half-map B.
File | emd_17184_half_map_2.map | ||||||||||||
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Annotation | Half-map B. | ||||||||||||
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Density Histograms |
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Sample components
+Entire : MYC-MAX bound to a nucleosome at SHL+5.8
+Supramolecule #1: MYC-MAX bound to a nucleosome at SHL+5.8
+Supramolecule #2: Nucleosomal core particle
+Supramolecule #3: cMYC/MAX heterodimer
+Supramolecule #4: Histone octamer
+Supramolecule #5: Nucleosomal DNA
+Macromolecule #1: Histone H3.1
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1-B/E
+Macromolecule #4: Histone H2B type 1-J
+Macromolecule #5: Histone H2A type 1-K
+Macromolecule #8: Myc proto-oncogene protein
+Macromolecule #9: Protein max
+Macromolecule #6: DNA (144-MER)
+Macromolecule #7: DNA (144-MER)
+Macromolecule #10: PENTANEDIAL
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |