7BRE

The crystal structure of MLL2 in complex with ASH2L and RBBP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 

Starting Models: experimental
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Literature

Crystal Structure of MLL2 Complex Guides the Identification of a Methylation Site on P53 Catalyzed by KMT2 Family Methyltransferases.

Li, Y.Zhao, L.Tian, X.Peng, C.Gong, F.Chen, Y.

(2020) Structure 28: 1141

  • DOI: https://doi.org/10.1016/j.str.2020.07.002
  • Primary Citation of Related Structures:  
    7BRE

  • PubMed Abstract: 

    KMT2 family methyltransferases methylate histone H3 lysine 4 and play essential roles in multiple cellular processes. MLL2 (KMT2B) is required for early epigenetic decisions during development and contributes to the methylation of bivalent promoters. Here, we determined the crystal structure of the MLL2 SET -RBBP5 AS-ABM -ASH2L SPRY complex and confirmed that RBBP5 AS-ABM -ASH2L SPRY was essential for activating the MLL2 SET domain through a conserved mechanism across KMT2 family complexes. In the MLL2 complex structure, a short N-terminal loop of MLL2 SET adopts a similar configuration of the H3 peptide and inserts into the substrate-binding pocket of another MLL2 SET , indicating a potential substrate for MLL2 SET . We identify that P53 contains a sequence similar to the N-terminal loop of MLL2 SET , and demonstrate that K305 of P53 could be methylated by KMT2 family complexes except for SET1A. Our results provide an important implication of functional interplay between P53 and KMT2 family complexes, and also suggest the possible broad landscape of non-histone substrate for KMT2 family methyltransferases.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2
A, D
184Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBL3 (Homo sapiens)
Explore Q9UBL3 
Go to UniProtKB:  Q9UBL3
PHAROS:  Q9UBL3
GTEx:  ENSG00000129691 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBL3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2BB,
C [auth E]
165Homo sapiensMutation(s): 0 
Gene Names: MLL2
EC: 2.1.1.354 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UMN6 (Homo sapiens)
Explore Q9UMN6 
Go to UniProtKB:  Q9UMN6
PHAROS:  Q9UMN6
GTEx:  ENSG00000272333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UMN6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5E [auth C],
F
27Homo sapiensMutation(s): 0 
Gene Names: RBBP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q15291 (Homo sapiens)
Explore Q15291 
Go to UniProtKB:  Q15291
PHAROS:  Q15291
GTEx:  ENSG00000117222 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15291
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  7BRE IC50: 2300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.075α = 90
b = 66.195β = 93.23
c = 83.734γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970576
National Natural Science Foundation of China (NSFC)China31900934

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Database references, Refinement description