39GO | pdb_000039go

Crystal structure of a bacterial DOT1L methyl-transferase in complex with S-adenosyl homocysteine

• PDB DOI: https://doi.org/10.2210/pdb39GO/pdb
• Entry: 39GO supersedes: 9NE1

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-10-07 Released: 2026-11-04 
• Deposition Author(s): Mondino, S., Dalla Rizza, J., Larrieux, N., Buschiazzo, A.
• Funding Organization(s): Fondation pour la Recherche Medicale (FRM), Pasteur Institute, Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: in silico

Literature

The bacterial effector LpDot1 methylates SFPQ to hijack paraspeckle dynamics and alternative splicing immune responses

Nicchi, S., Mondino, S., Rusniok, C., Mahtal, N., Raynal, B., ElJ, R., Quentin, G.G., Dalla Rizza, J., Larrieux, N., Martyn, J.E., Schoeler, H., Schmutz, S., Matondo, M., Buschiazzo, A., Buchrieser, C., Rolando, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.17 kDa 
• Atom Count: 1,684 
• Modeled Residue Count: 203 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase, H3 lysine-79 specific	A	227	Legionella pneumophila	Mutation(s): 0  Gene Names: D1H98_04800 EC: 2.1.1.360
UniProt
Find proteins for A0A3A6VYM1 (Legionella pneumophila subsp. pneumophila) Explore A0A3A6VYM1  Go to UniProtKB:  A0A3A6VYM1

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MLZ	A	LYS	Methylation	C7 H16 N2 O2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.409	α = 90
b = 69.409	β = 90
c = 80.698	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Mondino, S., Dalla Rizza, J., Larrieux, N., Buschiazzo, A.
• This entry supersedes: 9NE1

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Funding Organization	Location	Grant Number
Fondation pour la Recherche Medicale (FRM)	France	EQU201903007847
Pasteur Institute	France	PTR 395-20
Agence Nationale de la Recherche (ANR)	France	ANR-25-CE15-6707 ; ANR-10-LABX-62-IBEID ; ANR-20-PAMR-0011-TheraEPI ; ANR-18-CE15-0005-01

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release