Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42545.69 
• Atom Count: 2831 
• Residue Count: 369 
• Unique protein chains: 3

5F6L

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

• DOI: 10.2210/pdb5F6L/pdb

• Classification: PROTEIN BINDING/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 2 


• Deposited: 2015-12-06 Released: 2016-02-24 
• Deposition Author(s): Li, Y., Lei, M., Chen, Y.
• Funding Organization(s): Chinese Academy of Sciences 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.213 
• R-Value Work: 0.166 

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

• PubMed: 26886794 
• DOI: 10.1038/nature16952
• Primary Citation of Related Structures:  
  5F6K, 5F5E, 5F59


• 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
Retinoblastoma-binding protein 5	J	27	Homo sapiens	Mutation(s): 0  Gene Names: RBBP5 (RBQ3)
Find proteins for Q15291 (Homo sapiens) Go to Gene View: RBBP5 Go to UniProtKB:  Q15291

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Set1/Ash2 histone methyltransferase complex subunit ASH2	B	184	Homo sapiens	Mutation(s): 0  Gene Names: ASH2L (ASH2L1)
Find proteins for Q9UBL3 (Homo sapiens) Go to Gene View: ASH2L Go to UniProtKB:  Q9UBL3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase 2A	A	158	Homo sapiens	Mutation(s): 2  Gene Names: KMT2A (ALL1, CXXC7, HRX, HTRX, MLL, MLL1, TRX1) EC: 2.1.1.43
Find proteins for Q03164 (Homo sapiens) Go to Gene View: KMT2A Go to UniProtKB:  Q03164

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SAH	A	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.213 
• R-Value Work: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 74.966	α = 90.00
b = 44.410	β = 106.16
c = 117.792	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data collection
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB08010201

Revision History 

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