+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17183 | |||||||||
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Title | OCT4 and MYC-MAX co-bound to a nucleosome | |||||||||
Map data | Sharpened map (LocScale) | |||||||||
Sample |
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Keywords | TRANSCRIPTION | |||||||||
Function / homology | Function and homology information Mad-Max complex / SCF ubiquitin ligase complex binding / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling ...Mad-Max complex / SCF ubiquitin ligase complex binding / cell fate commitment involved in formation of primary germ layer / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / RNA polymerase II transcription repressor complex / endodermal cell fate specification / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / Specification of primordial germ cells / RUNX3 regulates WNT signaling / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Transcriptional regulation of pluripotent stem cells / negative regulation of cell division / negative regulation of monocyte differentiation / Germ layer formation at gastrulation / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / miRNA binding / 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 intrinsic apoptotic signaling pathway by p53 class mediator / somatic stem cell population maintenance / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / blastocyst development / MLL1 complex / negative regulation of tumor necrosis factor-mediated signaling pathway / chromosome organization / negative regulation of megakaryocyte differentiation / anatomical structure morphogenesis / protein localization to CENP-A containing chromatin / BMP signaling pathway / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Cyclin E associated events during G1/S transition / heterochromatin organization / epigenetic regulation of gene expression / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / : / 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 / ERK1 and ERK2 cascade / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / bioluminescence / DNA methylation / Condensation of Prophase Chromosomes / negative regulation of miRNA transcription / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / innate immune response in mucosa / generation of precursor metabolites and energy / Defective pyroptosis / transcription coregulator binding / positive regulation of epithelial cell proliferation / HDACs deacetylate histones / response to gamma radiation / RNA Polymerase I Promoter Escape / protein-DNA complex / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Michael AK / Stoos L / Kempf G / Cavadini S / Thoma N | |||||||||
Funding support | European Union, France, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17183.map.gz | 31.6 MB | EMDB map data format | |
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Header (meta data) | emd-17183-v30.xml emd-17183.xml | 31.5 KB 31.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17183_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_17183.png | 83.6 KB | ||
Others | emd_17183_additional_1.map.gz emd_17183_half_map_1.map.gz emd_17183_half_map_2.map.gz | 32.1 MB 59.4 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17183 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17183 | HTTPS FTP |
-Validation report
Summary document | emd_17183_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_17183_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_17183_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_17183_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17183 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17183 | HTTPS FTP |
-Related structure data
Related structure data | 8otsMC 8osjC 8oskC 8oslC 8ottC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_17183.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map (LocScale) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened full map
File | emd_17183_additional_1.map | ||||||||||||
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Annotation | Unsharpened full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_17183_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_17183_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : MYC-MAX and OCT4-bound nucleosome
+Supramolecule #1: MYC-MAX and OCT4-bound nucleosome
+Supramolecule #2: Nucleosomal core particle
+Supramolecule #3: Histone octamer
+Supramolecule #4: Nucleosomal DNA
+Supramolecule #5: Nucleosome-bound factors
+Supramolecule #6: OCT4
+Supramolecule #7: cMYC-MAX heterodimer
+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 #7: Green fluorescent protein,POU domain, class 5, transcription factor 1
+Macromolecule #8: Myc proto-oncogene protein
+Macromolecule #9: Protein max
+Macromolecule #5: DNA (127-MER)
+Macromolecule #6: DNA (127-MER)
+Macromolecule #10: PENTANEDIAL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |