9A3O | pdb_00009a3o

CLOCK-BMAL1 bound to a nucleosome at SHL -6.2


Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Cooperation between bHLH transcription factors and histones for DNA access

Michael, A.K.Stoos, L.Crosby, P.Eggers, N.Nie, X.Y.Makasheva, K.Minnich, M.Healy, K.L.Weiss, J.Kempf, G.Cavadini, S.Kater, L.Seebacher, J.Vecchia, L.Chakraborty, D.Isbel, L.Grand, R.G.Andersch, F.Fribourgh, J.L.Schuebeler, D.Zuber, J.Liu, A.C.Becker, P.B.Fierz, B.Partch, C.L.Menet, J.S.Thoma, N.H.

(2023) Nature 619: 385-393

  • DOI: https://doi.org/10.1038/s41586-023-06282-3
  • Primary Citation of Related Structures:  
    8OSJ, 8OSK, 8OSL, 8OTS, 8OTT, 9A3O, 9A3P

  • PubMed Abstract: 

    The basic helix-loop-helix (bHLH) family of transcription factors recognizes DNA motifs known as E-boxes (CANNTG) and includes 108 members 1 . 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. 2,3 ). 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 4 , the CLOCK-BMAL1 Per-Arnt-Sim (PAS) dimerization domains engage the histone octamer disc. Binding of tandem E-boxes 5-7 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.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.1
A, E
139Homo sapiensMutation(s): 0 
Gene Names: H3C1H3C2H3C3H3C4H3C6H3C7H3C8H3C10H3C11H3C12
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UniProt GroupP68431
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
B, F
106Homo sapiensMutation(s): 0 
Gene Names: 
H4C1H4C2H4C3H4C4H4C5H4C6H4C8H4C9H4C11H4C12...
H4C1H4C2H4C3H4C4H4C5H4C6H4C8H4C9H4C11H4C12H4C13H4C14H4C15H4C16

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A
C, G
133Homo sapiensMutation(s): 0 
Gene Names: H2AC4H2AC8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B
D, H
128Homo sapiensMutation(s): 0 
Gene Names: H2BC11
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian locomoter output cycles protein kaputK [auth M]375Mus musculusMutation(s): 0 
Gene Names: Clock
EC: 2.3.1.48
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IMPC:  MGI:99698
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Basic helix-loop-helix ARNT-like protein 1L [auth N]384Mus musculusMutation(s): 0 
Gene Names: Bmal1
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (128-MER)153N/A
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (128-MER)153N/A
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Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: No 
  • Multi-State: No 
  • Ordered State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

Structure Validation

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View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-01
    Type: Initial release