6PWW

Cryo-EM structure of MLL1 in complex with RbBP5 and WDR5 bound to the nucleosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



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:  
    6PWV, 6PWX, 6PWW

  • 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. uhnsoo@med.umich.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5A538Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
Find proteins for Q15291 (Homo sapiens)
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PHAROS  Q15291
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5B313Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
Find proteins for P61964 (Homo sapiens)
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PHAROS  P61964
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2AC209Homo sapiensMutation(s): 0 
Gene Names: KMT2AALL1CXXC7HRXHTRXMLLMLL1TRX1
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q03164 (Homo sapiens)
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PHAROS  Q03164
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.2GK136Xenopus laevisMutation(s): 1 
Find proteins for P84233 (Xenopus laevis)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4HL103Xenopus laevisMutation(s): 0 
Find proteins for P62799 (Xenopus laevis)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2A type 1IM129Xenopus laevisMutation(s): 0 
Find proteins for P06897 (Xenopus laevis)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1JN123Xenopus laevisMutation(s): 1 
Find proteins for P02281 (Xenopus laevis)
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Entity ID: 8
MoleculeChainsLengthOrganismImage
DNA (146-MER)O147synthetic construct
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Entity ID: 9
MoleculeChainsLengthOrganismImage
DNA (146-MER)P147synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
C
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

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C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHIC50:  2300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 

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