1MT6

Structure of histone H3 K4-specific methyltransferase SET7/9 with AdoHcy

• PDB DOI: https://doi.org/10.2210/pdb1MT6/pdb

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


• Deposited: 2002-09-20 Released: 2002-11-06 
• Deposition Author(s): Jacobs, S.A., Harp, J.M., Devarakonda, S., Kim, Y., Rastinejad, F., Khorasanizadeh, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 

Literature

The active site of the SET domain is constructed on a knot

Jacobs, S.A., Harp, J.M., Devarakonda, S., Kim, Y., Rastinejad, F., Khorasanizadeh, S.

(2002) Nat Struct Biol 9: 833-838

• PubMed: 12389038 
• DOI: https://doi.org/10.1038/nsb861
• Primary Citation of Related Structures:  
  1MT6, 1MUF


• PubMed Abstract: 
  

  The SET domain contains the catalytic center of lysine methyltransferases that target the N-terminal tails of histones and regulate chromatin function. Here we report the structure of the SET7/9 protein in the absence and presence of its cofactor product, S-adenosyl-L-homocysteine (AdoHcy). A knot within the SET domain helps form the methyltransferase active site, where AdoHcy binds and lysine methylation is likely to occur. A structure-guided comparison of sequences within the SET protein family suggests that the knot substructure and active site environment are conserved features of the SET domain.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.53 kDa 
• Atom Count: 2,389 
• Modelled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET9	A	280	Homo sapiens	Mutation(s): 0  EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens) Explore Q8WTS6  Go to UniProtKB:  Q8WTS6
PHAROS:  Q8WTS6 GTEx:  ENSG00000145391

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  1MT6	IC50: min: 3.00e+4, max: 4.70e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.263 
• R-Value Work: 0.226 
• R-Value Observed: 0.226 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.347	α = 90
b = 76.038	β = 90
c = 166.284	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-06 
Deposition Author(s): Jacobs, S.A., Harp, J.M., Devarakonda, S., Kim, Y., Rastinejad, F., Khorasanizadeh, S.

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations