6KIW

Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of nucleosome recognition and modification by MLL methyltransferases.

Xue, H.Yao, T.Cao, M.Zhu, G.Li, Y.Yuan, G.Chen, Y.Lei, M.Huang, J.

(2019) Nature 573: 445-449

  • DOI: 10.1038/s41586-019-1528-1
  • Primary Citation of Related Structures:  
    6KIU, 6KIW, 6KIV, 6KIX, 6KIZ

  • PubMed Abstract: 
  • Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development 1-6 ...

    Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development 1-6 . The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities 7-9 . Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown 10-12 . Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification.


    Organizational Affiliation

    Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. huangjing@shsmu.edu.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3A, E135Xenopus laevisMutation(s): 0 
Gene Names: XELAEV_18002543mg
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Find proteins for P84233 (Xenopus laevis)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H122Xenopus laevisMutation(s): 2 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2CK205Homo sapiensMutation(s): 1 
Gene Names: KMT2CHALRKIAA1506MLL3
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5L [auth N]538Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinM [auth O]76Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1
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PHAROS:  P62979
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5N [auth R]334Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2O [auth T]534Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
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PHAROS:  Q9UBL3
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (144-MER)I144synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J145synthetic construct
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
P [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other