1H3I | pdb_00001h3i

Crystal structure of the Histone Methyltransferase SET7/9

• PDB DOI: https://doi.org/10.2210/pdb1H3I/pdb

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


• Deposited: 2002-09-04 Released: 2002-11-11 
• Deposition Author(s): Wilson, J.R., Jing, C., Walker, P.A., Martin, S.R., Howell, S.A., Blackburn, G.M., Gamblin, S.J., Xiao, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.255 (Depositor) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Crystal Structure and Functional Analysis of the Histone Methyltransferase Set7/9

Wilson, J.R., Jing, C., Walker, P.A., Martin, S.R., Howell, S.A., Blackburn, G.M., Gamblin, S.J., Xiao, B.

(2002) Cell 111: 105

• PubMed: 12372304 
• DOI: https://doi.org/10.1016/s0092-8674(02)00964-9
• Primary Citation Related Structures: 
  1H3I


• PubMed Abstract: 
  

  Methylation of lysine residues in the N-terminal tails of histones is thought to represent an important component of the mechanism that regulates chromatin structure. The evolutionarily conserved SET domain occurs in most proteins known to possess histone lysine methyltransferase activity. We present here the crystal structure of a large fragment of human SET7/9 that contains a N-terminal beta-sheet domain as well as the conserved SET domain. Mutagenesis identifies two residues in the C terminus of the protein that appear essential for catalytic activity toward lysine-4 of histone H3. Furthermore, we show how the cofactor AdoMet binds to this domain and present biochemical data supporting the role of invariant residues in catalysis, binding of AdoMet, and interactions with the peptide substrate.

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Organizational Affiliation: 
• Structural Biology Group, National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 65.22 kDa 
• Atom Count: 4,935 
• Modeled Residue Count: 586 
• Deposited Residue Count: 586 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3 LYSINE 4 SPECIFIC METHYLTRANSFERASE	A, B	293	Homo sapiens	Mutation(s): 0  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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.255 (Depositor) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.09	α = 90
b = 82.83	β = 90
c = 116.15	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-11 
Deposition Author(s): Wilson, J.R., Jing, C., Walker, P.A., Martin, S.R., Howell, S.A., Blackburn, G.M., Gamblin, S.J., Xiao, B.

Revision History  

• Version 1.0: 2002-11-11
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations