5F6K

Crystal structure of the MLL3-Ash2L-RbBP5 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for activity regulation of MLL family methyltransferases.

Li, Y.Han, J.Zhang, Y.Cao, F.Liu, Z.Li, S.Wu, J.Hu, C.Wang, Y.Shuai, J.Chen, J.Cao, L.Li, D.Shi, P.Tian, C.Zhang, J.Dou, Y.Li, G.Chen, Y.Lei, M.

(2016) Nature 530: 447-452

  • DOI: https://doi.org/10.1038/nature16952
  • Primary Citation of Related Structures:  
    5F59, 5F5E, 5F6K, 5F6L

  • PubMed Abstract: 

    The mixed lineage leukaemia (MLL) family of proteins (including MLL1-MLL4, SET1A and SET1B) specifically methylate histone 3 Lys4, and have pivotal roles in the transcriptional regulation of genes involved in haematopoiesis and development. The methyltransferase activity of MLL1, by itself severely compromised, is stimulated by the three conserved factors WDR5, RBBP5 and ASH2L, which are shared by all MLL family complexes. However, the molecular mechanism of how these factors regulate the activity of MLL proteins still remains poorly understood. Here we show that a minimized human RBBP5-ASH2L heterodimer is the structural unit that interacts with and activates all MLL family histone methyltransferases. Our structural, biochemical and computational analyses reveal a two-step activation mechanism of MLL family proteins. These findings provide unprecedented insights into the common theme and functional plasticity in complex assembly and activity regulation of MLL family methyltransferases, and also suggest a universal regulation mechanism for most histone methyltransferases.


  • Organizational Affiliation

    National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2
A, B
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2C
C, E
159Homo sapiensMutation(s): 0 
Gene Names: KMT2CHALRKIAA1506MLL3
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEZ4 (Homo sapiens)
Explore Q8NEZ4 
Go to UniProtKB:  Q8NEZ4
PHAROS:  Q8NEZ4
GTEx:  ENSG00000055609 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEZ4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5
D, F
27Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
peptide ARTKQTARKG [auth M]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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.342α = 90
b = 236.076β = 90
c = 44.416γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Strategic Priority Research Program of the Chinese Academy of SciencesChinaXDB08010201

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description