8OSL

Cryo-EM structure of CLOCK-BMAL1 bound to the native Por enhancer nucleosome (map 2, additional 3D classification and flexible refinement)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 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.S.Andersch, F.Fribourgh, J.L.Schubeler, 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

  • 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: 
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Find proteins for P68431 (Homo sapiens)
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PHAROS:  P68431
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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: 
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Find proteins for P62805 (Homo sapiens)
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PHAROS:  P62805
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1-B/E
C, G
133Homo sapiensMutation(s): 0 
Gene Names: HIST1H2ABH2AFMHIST1H2AEH2AFA
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PHAROS:  P04908
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-J
D, H
128Homo sapiensMutation(s): 0 
Gene Names: HIST1H2BJH2BFR
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens)
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GTEx:  ENSG00000124635 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Circadian locomoter output cycles protein kaputK [auth M],
M [auth O]
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],
N [auth P]
384Mus musculusMutation(s): 0 
Gene Names: Bmal1Arntl
UniProt
Find proteins for Q9WTL8 (Mus musculus)
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (147-MER)147Homo sapiens
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTRosettaEM
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union884331
Human Frontier Science Program (HFSP)FranceLT000646/2018-L5

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references, Structure summary
  • Version 1.2: 2023-07-12
    Changes: Database references
  • Version 1.3: 2023-07-19
    Changes: Database references
  • Version 1.4: 2023-07-26
    Changes: Database references
  • Version 1.5: 2024-07-24
    Changes: Data collection, Refinement description