6KIU

Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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, 6KIV, 6KIW, 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
UniProt
Find proteins for P84233 (Xenopus laevis)
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UniProt GroupP84233
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B, F102Xenopus laevisMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2AC, G129Xenopus laevisMutation(s): 0 
Gene Names: hist1h2ajLOC494591XELAEV_18003602mg
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Find proteins for P06897 (Xenopus laevis)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H2B 1.1D, H122Xenopus laevisMutation(s): 2 
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UniProt GroupP02281
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2AK216Homo sapiensMutation(s): 0 
Gene Names: KMT2AALL1CXXC7HRXHTRXMLLMLL1TRX1
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
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PHAROS:  Q03164
GTEx:  ENSG00000118058 
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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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GTEx:  ENSG00000117222 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5M [auth R]334Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
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GTEx:  ENSG00000196363 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2N [auth T]534Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
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GTEx:  ENSG00000129691 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinO76Homo sapiensMutation(s): 1 
Gene Names: RPS27AUBA80UBCEP1
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GTEx:  ENSG00000143947 
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Entity ID: 5
MoleculeChainsLengthOrganismImage
DNA (145-MER)I 145synthetic construct
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (145-MER)J 145synthetic construct
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

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P [auth K]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
LYS
Query on LYS

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R [auth K]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
GLN
Query on GLN

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S [auth K]GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-VKHMYHEASA-N
 Ligand Interaction
ZN
Query on ZN

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Q [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  6KIU IC50: 2300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National 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