9NE1 | pdb_00009ne1

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

• PDB DOI: https://doi.org/10.2210/pdb9NE1/pdb

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


• Deposited: 2025-02-19 Released: 2026-02-25 
• Deposition Author(s): Mondino, S., Dalla Rizza, J., Larrieux, N., Buschiazzo, A.
• Funding Organization(s): Pasteur Institute

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: in silico

Literature

A bacterial DOT1-like methyltransferase subverts paraspeckle dynamics and host cell splicing events

Nicchi, S., Mondino, S., Rusniok, C., Danckaert, A., Schoeler, H., Martyn, E.J., Dalla Rizza, J., Larrieux, N., Mahtal, N., Quentin, G.G., 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.17 kDa 
• Atom Count: 1,683 
• 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	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	A	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.270 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.444	α = 90
b = 69.444	β = 90
c = 80.769	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Mondino, S., Dalla Rizza, J., Larrieux, N., Buschiazzo, A.

---

Funding Organization	Location	Grant Number
Pasteur Institute	France	PTR 2020 #395

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release