6PWV

Cryo-EM structure of MLL1 core complex bound to the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 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

Cryo-EM structure of the human MLL1 core complex bound to the nucleosome.

Park, S.H.Ayoub, A.Lee, Y.T.Xu, J.Kim, H.Zheng, W.Zhang, B.Sha, L.An, S.Zhang, Y.Cianfrocco, M.A.Su, M.Dou, Y.Cho, U.S.

(2019) Nat Commun 10: 5540-5540

  • DOI: https://doi.org/10.1038/s41467-019-13550-2
  • Primary Citation of Related Structures:  
    6PWV, 6PWW, 6PWX

  • PubMed Abstract: 

    Mixed lineage leukemia (MLL) family histone methyltransferases are enzymes that deposit histone H3 Lys4 (K4) mono-/di-/tri-methylation and regulate gene expression in mammals. Despite extensive structural and biochemical studies, the molecular mechanisms whereby the MLL complexes recognize histone H3K4 within nucleosome core particles (NCPs) remain unclear. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the NCP-bound human MLL1 core complex. We show that the MLL1 core complex anchors to the NCP via the conserved RbBP5 and ASH2L, which interact extensively with nucleosomal DNA and the surface close to the N-terminal tail of histone H4. Concurrent interactions of RbBP5 and ASH2L with the NCP uniquely align the catalytic MLL1 SET domain at the nucleosome dyad, thereby facilitating symmetrical access to both H3K4 substrates within the NCP. Our study sheds light on how the MLL1 complex engages chromatin and how chromatin binding promotes MLL1 tri-methylation activity.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, 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: 2.1.1.43
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Find proteins for Q03164 (Homo sapiens)
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.2D [auth G],
H [auth K]
136Xenopus laevisMutation(s): 1 
UniProt
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4E [auth H],
I [auth L]
103Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1F [auth I],
J [auth M]
129Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B 1.1G [auth J],
K [auth N]
122Xenopus laevisMutation(s): 0 
UniProt
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Protein dpy-30 homologN [auth E],
O [auth F]
102Homo sapiensMutation(s): 0 
Gene Names: DPY30
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Find proteins for Q9C005 (Homo sapiens)
Go to UniProtKB:  Q9C005
PHAROS:  Q9C005
GTEx:  ENSG00000162961 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2P [auth D]534Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
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Find proteins for Q9UBL3 (Homo sapiens)
Go to UniProtKB:  Q9UBL3
PHAROS:  Q9UBL3
GTEx:  ENSG00000129691 
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Entity ID: 8
MoleculeChains LengthOrganismImage
DNA (147-MER)L [auth O]147synthetic construct
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Entity ID: 9
MoleculeChains LengthOrganismImage
DNA (147-MER)M [auth P]147synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.20 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 Research Foundation (NRF, Korea)Korea, Republic OfNRF-2015M3D3A1A01064876

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Structure summary
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references, Other