5F6L

The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 

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:  
    5F59, 5F5E, 5F6L, 5F6K

  • 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 methyltra ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinoblastoma-binding protein 5 J27Homo sapiensMutation(s): 0 
Gene Names: RBBP5, RBQ3
Find proteins for Q15291 (Homo sapiens)
Explore Q15291 
Go to UniProtKB:  Q15291
NIH Common Fund Data Resources
PHAROS:  Q15291
GTEx:  ENSG00000117222
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Set1/Ash2 histone methyltransferase complex subunit ASH2 B184Homo sapiensMutation(s): 0 
Gene Names: ASH2L, ASH2L1
Find proteins for Q9UBL3 (Homo sapiens)
Explore Q9UBL3 
Go to UniProtKB:  Q9UBL3
NIH Common Fund Data Resources
PHAROS:  Q9UBL3
GTEx:  ENSG00000129691
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2A A158Homo sapiensMutation(s): 2 
Gene Names: KMT2A, ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q03164 (Homo sapiens)
Explore Q03164 
Go to UniProtKB:  Q03164
NIH Common Fund Data Resources
PHAROS:  Q03164
GTEx:  ENSG00000118058
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 Ideal Coordinates CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHIC50:  2300   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.966α = 90
b = 44.41β = 106.16
c = 117.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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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
Chinese Academy of SciencesChinaXDB08010201

Revision History 

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