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- PDB-8osj: Cryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at ... -

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Entry
Database: PDB / ID: 8osj
TitleCryo-EM structure of CLOCK-BMAL1 bound to a nucleosomal E-box at position SHL-6.2 (DNA conformation 1)
Components
  • (DNA (124-MER)) x 2
  • Basic helix-loop-helix ARNT-like protein 1
  • Circadian locomoter output cycles protein kaput
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • Histone H3.1
  • Histone H4
KeywordsGENE REGULATION / E-box / transcription factor / circadian clock
Function / homology
Function and homology information


CLOCK-BMAL transcription complex / positive regulation of skeletal muscle cell differentiation / regulation of hair cycle / positive regulation of protein acetylation / NPAS4 regulates expression of target genes / maternal process involved in parturition / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / 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 / positive regulation of protein acetylation / NPAS4 regulates expression of target genes / maternal process involved in parturition / negative regulation of nuclear receptor-mediated glucocorticoid signaling pathway / regulation of type B pancreatic cell development / bHLH transcription factor binding / regulation of cellular senescence / chromatoid body / positive regulation of circadian rhythm / oxidative stress-induced premature senescence / negative regulation of TOR signaling / response to redox state / negative regulation of cold-induced thermogenesis / protein acetylation / negative regulation of fat cell differentiation / regulation of protein catabolic process / E-box binding / regulation of neurogenesis / negative regulation of tumor necrosis factor-mediated signaling pathway / histone acetyltransferase activity / negative regulation of megakaryocyte differentiation / histone acetyltransferase / protein localization to CENP-A containing chromatin / energy homeostasis / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / regulation of insulin secretion / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / DNA damage checkpoint signaling / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / cellular response to ionizing radiation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / transcription coregulator activity / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / circadian regulation of gene expression / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / positive regulation of NF-kappaB transcription factor activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / circadian rhythm / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / regulation of circadian rhythm / PML body / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / chromatin DNA binding / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / autophagy / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / positive regulation of inflammatory response / protein import into nucleus / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / positive regulation of canonical Wnt signaling pathway / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
Similarity search - Function
: / : / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...: / : / Nuclear translocator / Helix-loop-helix DNA-binding domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Circadian locomoter output cycles protein kaput / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.1 / Basic helix-loop-helix ARNT-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsMichael, A.K. / Stoos, L. / Kempf, G. / Cavadini, S. / Thoma, N.H.
Funding supportEuropean Union, Switzerland, France, 5items
OrganizationGrant numberCountry
European Research Council (ERC)884331European Union
Swiss National Science FoundationCRSII5_186230 Switzerland
Swiss National Science Foundation31003A_179541 Switzerland
Swiss National Science Foundation310030_201206 Switzerland
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct / Item: _citation.title / _struct.title
Revision 1.2Jul 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Jul 19, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.1
B: Histone H4
C: Histone H2A type 1-B/E
D: Histone H2B type 1-J
E: Histone H3.1
F: Histone H4
G: Histone H2A type 1-B/E
H: Histone H2B type 1-J
I: DNA (124-MER)
J: DNA (124-MER)
M: Circadian locomoter output cycles protein kaput
N: Basic helix-loop-helix ARNT-like protein 1


Theoretical massNumber of molelcules
Total (without water)293,91012
Polymers293,91012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 10 molecules AEBFCGDHMN

#1: Protein Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 15719.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#2: Protein Histone H4


Mass: 11676.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 14447.825 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 14088.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H2BJ, H2BFR / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein Circadian locomoter output cycles protein kaput / mCLOCK


Mass: 43768.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Clock / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O08785, histone acetyltransferase
#8: Protein Basic helix-loop-helix ARNT-like protein 1 / Arnt3 / Aryl hydrocarbon receptor nuclear translocator-like protein 1 / Brain and muscle ARNT-like 1


Mass: 43821.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bmal1, Arntl / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9WTL8

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (124-MER)


Mass: 47029.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (124-MER)


Mass: 47426.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1CLOCK-BMAL1 bound to a nucleosome at SHL -6.2COMPLEXall0MULTIPLE SOURCES
2Nucleosome core particleCOMPLEX#1-#61MULTIPLE SOURCES
3Histone octamerCOMPLEX#1-#42RECOMBINANT
4Nucleosomal DNACOMPLEX#5-#62RECOMBINANT
5CLOCK-BMAL1 heterodimerCOMPLEX#7-#81RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
33Homo sapiens (human)9606
44synthetic construct (others)32630
55Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
33Escherichia coli (E. coli)562
44synthetic construct (others)32630
55Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152914 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00718307
ELECTRON MICROSCOPYf_angle_d0.67726012
ELECTRON MICROSCOPYf_dihedral_angle_d24.7537363
ELECTRON MICROSCOPYf_chiral_restr0.0472929
ELECTRON MICROSCOPYf_plane_restr0.0052230

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