6W5N

Cryo-EM structure of MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nucleosome (Class05)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism for DPY30 and ASH2L intrinsically disordered regions to modulate the MLL/SET1 activity on chromatin.

Lee, Y.T.Ayoub, A.Park, S.H.Sha, L.Xu, J.Mao, F.Zheng, W.Zhang, Y.Cho, U.S.Dou, Y.

(2021) Nat Commun 12: 2953-2953

  • DOI: https://doi.org/10.1038/s41467-021-23268-9
  • Primary Citation of Related Structures:  
    6W5I, 6W5M, 6W5N

  • PubMed Abstract: 

    Recent cryo-EM structures show the highly dynamic nature of the MLL1-NCP (nucleosome core particle) interaction. Functional implication and regulation of such dynamics remain unclear. Here we show that DPY30 and the intrinsically disordered regions (IDRs) of ASH2L work together in restricting the rotational dynamics of the MLL1 complex on the NCP. We show that DPY30 binding to ASH2L leads to stabilization and integration of ASH2L IDRs into the MLL1 complex and establishes new ASH2L-NCP contacts. The significance of ASH2L-DPY30 interactions is demonstrated by requirement of both ASH2L IDRs and DPY30 for dramatic increase of processivity and activity of the MLL1 complex. This DPY30 and ASH2L-IDR dependent regulation is NCP-specific and applies to all members of the MLL/SET1 family of enzymes. We further show that DPY30 is causal for de novo establishment of H3K4me3 in ESCs. Our study provides a paradigm of how H3K4me3 is regulated on chromatin and how H3K4me3 heterogeneity can be modulated by ASH2L IDR interacting proteins.


  • Organizational Affiliation

    Department of Pathology, University of Michigan, Ann Arbor, MI, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5538Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15291 (Homo sapiens)
Go to UniProtKB:  Q15291
PHAROS:  Q15291
GTEx:  ENSG00000117222 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5313Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Go to UniProtKB:  P61964
PHAROS:  P61964
GTEx:  ENSG00000196363 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2A209Homo sapiensMutation(s): 0 
Gene Names: KMT2AALL1CXXC7HRXHTRXMLLMLL1TRX1
EC: 2.1.1.354
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens)
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2534Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBL3 (Homo sapiens)
Go to UniProtKB:  Q9UBL3
PHAROS:  Q9UBL3
GTEx:  ENSG00000129691 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2E [auth G],
I [auth K]
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4F [auth H],
J [auth L]
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1G [auth I],
K [auth M]
129Xenopus laevisMutation(s): 2 
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1H [auth J],
L [auth N]
123Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (147-MER)M [auth O]147synthetic construct
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Entity ID: 10
MoleculeChains LengthOrganismImage
DNA (147-MER)N [auth P]147synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesDK111465
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA250329

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2022-10-12
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection