1N3J | pdb_00001n3j

Structure and Substrate of a Histone H3 Lysine Methyltransferase from Paramecium Bursaria Chlorella Virus 1


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: mimized average structure 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3.

Manzur, K.L.Farooq, A.Zeng, L.Plotnikova, O.Koch, A.W.SachchidanandZhou, M.-M.

(2003) Nat Struct Biol 10: 187-196

  • DOI: https://doi.org/10.1038/nsb898
  • Primary Citation Related Structures: 
    1N3J

  • PubMed Abstract: 

    Site-specific lysine methylation of histones by SET domains is a hallmark for epigenetic control of gene transcription in eukaryotic organisms. Here we report that a SET domain protein from Paramecium bursaria chlorella virus can specifically di-methylate Lys27 in histone H3, a modification implicated in gene silencing. The solution structure of the viral SET domain reveals a butterfly-shaped head-to-head symmetric dimer different from other known protein methyltransferases. Each subunit consists of a Greek-key antiparallel beta-barrel and a three-stranded open-faced sandwich that mediates the dimer interface. Cofactor S-adenosyl-L-methionine (SAM) binds at the opening of the beta-barrel, and amino acids C-terminal to Lys27 in H3 and in the flexible C-terminal tail of the enzyme confer the specificity of this viral histone methyltransferase.


  • Organizational Affiliation
    • Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, One Gustave L. Levy Place, New York, New York 10029, USA.

Macromolecule Content 

  • Total Structure Weight: 27.21 kDa 
  • Atom Count: 1,912 
  • Modeled Residue Count: 238 
  • Deposited Residue Count: 238 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone H3 Lysine Methyltransferase
A, B
119Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A612L
UniProt
Find proteins for O41094 (Paramecium bursaria Chlorella virus 1)
Explore O41094 
Go to UniProtKB:  O41094
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41094
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 
  • Selection Criteria: mimized average structure 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-28
    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: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-05-22
    Changes: Data collection