Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 23.94 kDa 
• Atom Count: 1628 
• Residue Count: 188 
• Unique protein chains: 2

2W5Z

Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor product S-Adenosylhomocysteine and histone peptide.

• DOI: 10.2210/pdb2W5Z/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-12-15 Released: 2009-02-10 
• Deposition Author(s): Southall, S.M., Wong, P.S., Odho, Z., Roe, S.M., Wilson, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Structural Basis for the Requirement of Additional Factors for Mll1 Set Domain Activity and Recognition of Epigenetic Marks.

Southall, S.M., Wong, P.S., Odho, Z., Roe, S.M., Wilson, J.R.

(2009) Mol Cell 33: 181

• PubMed: 19187761 
• DOI: 10.1016/j.molcel.2008.12.029
• Primary Citation of Related Structures:  
  2W5Y, 2W5Z


• PubMed Abstract: 
  

The mixed-lineage leukemia protein MLL1 is a transcriptional regulator with an essential role in early development and hematopoiesis. The biological function of MLL1 is mediated by the histone H3K4 methyltransferase activity of the carboxyl-terminal SET domain. We have determined the crystal structure of the MLL1 SET domain in complex with cofactor product AdoHcy and a histone H3 peptide. This structure indicates that, in order to form a well-ordered active site, a highly variable but essential component of the SET domain must be repositioned. To test this idea, we compared the effect of the addition of MLL complex members on methyltransferase activity and show that both RbBP5 and Ash2L but not Wdr5 stimulate activity. Additionally, we have determined the effect of posttranslational modifications on histone H3 residues downstream and upstream from the target lysine and provide a structural explanation for why H3T3 phosphorylation and H3K9 acetylation regulate activity.

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Organizational Affiliation: 

Institute of Cancer Research, Chester Beatty Laboratories, Chelsea, London, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE-LYSINE N-METHYLTRANSFERASE HRX	A	192	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE PEPTIDE	C	9	Homo sapiens	Mutation(s): 0  EC: 2.1.1.43
Find proteins for P68433 (Mus musculus) Explore P68433  Go to UniProtKB:  P68433

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	A	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	C	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAH	IC50:  2300   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.247 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.95	α = 90
b = 56.55	β = 90
c = 78.41	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-12-15 
• Released Date: 2009-02-10 
Deposition Author(s): Southall, S.M., Wong, P.S., Odho, Z., Roe, S.M., Wilson, J.R.

Revision History 

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance