1MUF | pdb_00001muf

Structure of histone H3 K4-specific methyltransferase SET7/9

• PDB DOI: https://doi.org/10.2210/pdb1MUF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-09-23 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: 2.26 Å
• R-Value Free: 
  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

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 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: 28.94 kDa 
• Atom Count: 2,156 
• Modeled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET9	A	257	Homo sapiens	Mutation(s): 6  EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens) Explore Q8WTS6  Go to UniProtKB:  Q8WTS6
PHAROS:  Q8WTS6 GTEx:  ENSG00000145391

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.973	α = 90
b = 110.973	β = 90
c = 96.05	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data reduction
RESOLVE	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: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary