6PWX

Cryo-EM structure of RbBP5 bound to the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41467-019-13550-2
  • Primary Citation of Related Structures:  

  • 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 mechan ...

    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.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. yalid@med.umich.edu.,Department of Pathology, University of Michigan, Ann Arbor, Michigan, 48109, USA. yalid@med.umich.edu.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA. uhnsoo@med.umich.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-binding protein 5
A
538Homo sapiensMutation(s): 0 
Gene Names: RBBP5 (RBQ3)
Find proteins for Q15291 (Homo sapiens)
Go to Gene View: RBBP5
Go to UniProtKB:  Q15291
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.2
G, K
136Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
Go to UniProtKB:  P84233
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H4
H, L
103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
Go to UniProtKB:  P62799
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H2A type 1
I, M
129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
Go to UniProtKB:  P06897
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Histone H2B 1.1
J, N
123Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
Go to UniProtKB:  P02281
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (146-MER)O147synthetic construct
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (146-MER)P147synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
phenix.real_space_refinerefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-12-18
    Type: Initial release