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 

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
  • Structures With Same Primary Citation

  • 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

    Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, 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 ASH2A, B184Homo sapiensMutation(s): 0 
Gene Names: ASH2LASH2L1
Find proteins for Q9UBL3 (Homo sapiens)
Explore Q9UBL3 
Go to UniProtKB:  Q9UBL3
NIH Common Fund Data Resources
PHAROS  Q9UBL3
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase 2CC, E159Homo sapiensMutation(s): 0 
Gene Names: KMT2CHALRKIAA1506MLL3
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q8NEZ4 (Homo sapiens)
Explore Q8NEZ4 
Go to UniProtKB:  Q8NEZ4
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PHAROS  Q8NEZ4
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-binding protein 5D, F27Homo sapiensMutation(s): 0 
Gene Names: RBBP5RBQ3
Find proteins for Q15291 (Homo sapiens)
Explore Q15291 
Go to UniProtKB:  Q15291
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PHAROS  Q15291
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
peptide ARTKQTARKM9Homo sapiensMutation(s): 0 
Gene Names: H3-5H3F3C
Find proteins for Q6NXT2 (Homo sapiens)
Explore Q6NXT2 
Go to UniProtKB:  Q6NXT2
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PHAROS  Q6NXT2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
C, E
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
C, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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



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
    Changes: Database references