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Yorodumi- EMDB-17157: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17157 | |||||||||
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Title | Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL+5.8 (composite map) | |||||||||
Map data | Composite map generated from two maps. | |||||||||
Sample |
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Keywords | E-box / transcription factor / circadian clock / GENE REGULATION | |||||||||
Function / homology | Function and homology information CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / NPAS4 regulates expression of target genes / positive regulation of protein acetylation / negative regulation of glucocorticoid receptor signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence ...CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / NPAS4 regulates expression of target genes / positive regulation of protein acetylation / negative regulation of glucocorticoid receptor signaling pathway / maternal process involved in parturition / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence / aryl hydrocarbon receptor complex / perichromatin fibrils / chromatoid body / E-box binding / positive regulation of circadian rhythm / negative regulation of TOR signaling / oxidative stress-induced premature senescence / negative regulation of cold-induced thermogenesis / response to redox state / negative regulation of fat cell differentiation / protein acetylation / regulation of protein catabolic process / protein localization to CENP-A containing chromatin / regulation of insulin secretion / CENP-A containing nucleosome / regulation of neurogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / energy homeostasis / linoleic acid metabolic process / histone acetyltransferase activity / Meiotic synapsis / histone acetyltransferase / Inhibition of DNA recombination at telomere / transcription coregulator activity / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / HCMV Late Events / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / DNA damage checkpoint signaling / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / regulation of circadian rhythm / cellular response to ionizing radiation / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / circadian regulation of gene expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / circadian rhythm / heterochromatin formation / PML body / chromatin DNA binding / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / autophagy / positive regulation of inflammatory response / structural constituent of chromatin / positive regulation of canonical Wnt signaling pathway / protein import into nucleus / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Stoos L / Michael AK / Kempf G / Cavadini S / Thoma NH | |||||||||
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_17157.map.gz | 160.5 MB | EMDB map data format | |
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Header (meta data) | emd-17157-v30.xml emd-17157.xml | 26.1 KB 26.1 KB | Display Display | EMDB header |
Images | emd_17157.png | 45.9 KB | ||
Filedesc metadata | emd-17157.cif.gz | 7.5 KB | ||
Others | emd_17157_additional_1.map.gz | 147.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17157 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17157 | HTTPS FTP |
-Related structure data
Related structure data | 8oskMC 8osjC 8oslC 8otsC 8ottC C: citing same article (ref.) M: atomic model generated by this map |
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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_17157.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Composite map generated from two maps. | ||||||||||||||||||||
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: Composite map generated from two maps.
File | emd_17157_additional_1.map | ||||||||||||
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Annotation | Composite map generated from two maps. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CLOCK-BMAL1 bound to a nucleosome SHL+5.8
+Supramolecule #1: CLOCK-BMAL1 bound to a nucleosome SHL+5.8
+Supramolecule #2: Nucleosomal core particle
+Supramolecule #3: Histone octamer
+Supramolecule #4: Nucleosomal DNA
+Supramolecule #5: CLOCK-BMAL1 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: Circadian locomoter output cycles protein kaput
+Macromolecule #8: Basic helix-loop-helix ARNT-like protein 1
+Macromolecule #5: DNA (124-MER)
+Macromolecule #6: DNA (124-MER)
-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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25483 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |