5F6K

Crystal structure of the MLL3-Ash2L-RbBP5 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nature16952
  • Primary Citation of Related Structures:  

  • 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 methy ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Set1/Ash2 histone methyltransferase complex subunit ASH2,Set1/Ash2 histone methyltransferase complex subunit ASH2
A, B
184Homo sapiensMutation(s): 0 
Gene Names: ASH2L (ASH2L1)
Find proteins for Q9UBL3 (Homo sapiens)
Go to Gene View: ASH2L
Go to UniProtKB:  Q9UBL3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase 2C
C, E
159Homo sapiensMutation(s): 0 
Gene Names: KMT2C (HALR, KIAA1506, MLL3)
EC: 2.1.1.43
Find proteins for Q8NEZ4 (Homo sapiens)
Go to Gene View: KMT2C
Go to UniProtKB:  Q8NEZ4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-binding protein 5
D, F
27Homo sapiensMutation(s): 0 
Gene Names: RBBP5 (RBQ3)
Find proteins for Q15291 (Homo sapiens)
Go to Gene View: RBBP5
Go to UniProtKB:  Q15291
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptide ARTKQTARK
M
9Homo sapiensMutation(s): 0 
Gene Names: H3F3C
Find proteins for Q6NXT2 (Homo sapiens)
Go to Gene View: H3F3C
Go to UniProtKB:  Q6NXT2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
C, E
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.411 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 80.342α = 90.00
b = 236.076β = 90.00
c = 44.416γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-12-06 
  • Released Date: 2016-02-24 
  • Deposition Author(s): Li, Y., Lei, M., Chen, Y.

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

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references