7W6I

The crystal structure of MLL1 (N3861I/Q3867L/C3882SS)-RBBP5-ASH2L in complex with H3K4me1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for product specificities of MLL family methyltransferases.

Li, Y.Zhao, L.Zhang, Y.Wu, P.Xu, Y.Mencius, J.Zheng, Y.Wang, X.Xu, W.Huang, N.Ye, X.Lei, M.Shi, P.Tian, C.Peng, C.Li, G.Liu, Z.Quan, S.Chen, Y.

(2022) Mol Cell 82: 3810-3825.e8

  • DOI: https://doi.org/10.1016/j.molcel.2022.08.022
  • Primary Citation of Related Structures:  
    7W67, 7W6A, 7W6I, 7W6J, 7W6L

  • PubMed Abstract: 

    Human mixed-lineage leukemia (MLL) family methyltransferases methylate histone H3 lysine 4 to different methylation states (me1/me2/me3) with distinct functional outputs, but the mechanism underlying the different product specificities of MLL proteins remains unclear. Here, we develop methodologies to quantitatively measure the methylation rate difference between mono-, di-, and tri-methylation steps and demonstrate that MLL proteins possess distinct product specificities in the context of the minimum MLL-RBBP5-ASH2L complex. Comparative structural analyses of MLL complexes by X-ray crystal structures, fluorine-19 nuclear magnetic resonance, and molecular dynamics simulations reveal that the dynamics of two conserved tyrosine residues at the "F/Y (phenylalanine/tyrosine) switch" positions fine-tune the product specificity. The variation in the intramolecular interaction between SET-N and SET-C affects the F/Y switch dynamics, thus determining the product specificities of MLL proteins. These results indicate a modified F/Y switch rule applicable for most SET domain methyltransferases and implicate the functional divergence of MLL proteins.


  • 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; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai 200237, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2184Homo 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 2AB [auth C]159Homo sapiensMutation(s): 3 
Gene Names: KMT2AALL1CXXC7HRXHTRXMLLMLL1TRX1
EC: 2.1.1.364 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens)
Explore Q03164 
Go to UniProtKB:  Q03164
PHAROS:  Q03164
GTEx:  ENSG00000118058 
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UniProt GroupQ03164
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5C [auth F]27Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
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Find proteins for Q15291 (Homo sapiens)
Explore Q15291 
Go to UniProtKB:  Q15291
PHAROS:  Q15291
GTEx:  ENSG00000117222 
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UniProt GroupQ15291
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3CD [auth B]9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens)
Explore Q6NXT2 
Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2
GTEx:  ENSG00000188375 
Entity Groups  
UniProt GroupQ6NXT2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
D [auth B]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  7W6I IC50: 2300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.777α = 90
b = 44.422β = 107.51
c = 120.097γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37010303
National Natural Science Foundation of China (NSFC)China31670748
National Natural Science Foundation of China (NSFC)China31970576
National Natural Science Foundation of China (NSFC)China32071195
National Natural Science Foundation of China (NSFC)China31900934

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-11-02
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description