9Z2N | pdb_00009z2n

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)

• PDB DOI: https://doi.org/10.2210/pdb9Z2N/pdb
• EM Map EMD-73772: EMDB EMDataResource

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


• Deposited: 2025-11-05 Released: 2026-06-03 
• Deposition Author(s): Canepa, J., Ruiz-Arroyo, V.M., Nam, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), American Cancer Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental

Literature

Substrate selectivity of the human RNA m5C methyltransferase NSUN2

Canepa, J., Ruiz-Arroyo, V.M., Schlamowitz, N., Nam, Y.

(2026) Nature 

• DOI: https://doi.org/10.1038/s41586-026-10582-9

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 113.28 kDa 
• Atom Count: 6,481 
• Modeled Residue Count: 676 
• Deposited Residue Count: 858 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA cytosine C(5)-methyltransferase NSUN2	A	782	Homo sapiens	Mutation(s): 1  Gene Names: NSUN2, SAKI, TRM4 EC: 2.1.1 (PDB Primary Data), 2.1.1.203 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q08J23 (Homo sapiens) Explore Q08J23  Go to UniProtKB:  Q08J23
PHAROS:  Q08J23 GTEx:  ENSG00000037474

Entity ID: 2
Molecule	Chains	Length	Organism	Image
tRNA Lys(CTT)	B	76	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.57 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Canepa, J., Ruiz-Arroyo, V.M., Nam, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM122960
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA258589
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01ES038329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32GM131963
Welch Foundation	United States	I-2115-20220331
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP210041
American Cancer Society	United States	PF-24-1308804-01-RMC
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RP170644

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release