9Z2W | pdb_00009z2w

CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (No D-arm conformation)

  • 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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: in silico, experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9Z2W

This is version 1.1 of the entry. See complete history

Literature

Substrate selectivity of the human RNA m 5 C methyltransferase NSUN2.

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

(2026) Nature 

  • DOI: https://doi.org/10.1038/s41586-026-10582-9
  • Primary Citation Related Structures: 
    9Z2N, 9Z2O, 9Z2P, 9Z2Q, 9Z2R, 9Z2T, 9Z2U, 9Z2W, 9Z3D

  • PubMed Abstract: 

    Specific deposition of RNA modifications is important for regulating gene expression 1,2 . 5-Methylcytosine (m 5 C) is a common epitranscriptomic modification, and NSUN2 is a key enzyme responsible for m 5 C methylation of various types of RNA. Dysregulation of NSUN2 is associated with numerous diseases, including cancers and neurological disorders 3 . The versatility of NSUN2 complicates our understanding of its substrate specificity and molecular roles in biology and disease. Here we show how NSUN2 interacts with RNA substrates at distinct stages of its catalytic cycle to modify cytidines. Furthermore, we show the role of RNA structure in facilitating NSUN2 activity at multiple tRNA positions. We identify RNA duplexes surrounding the m 5 C modification site as crucial recognition elements for methylation, which enabled us to derive a minimized substrate that captures the preferred features of an NSUN2 substrate-a dual-stem structure containing the CNNRR motif at the 5' end of the first stem. Insights into the mechanisms underlying substrate-specific NSUN2 enzymatic activity provide opportunities for understanding and therapeutically targeting NSUN2-dependent methylation. Overall, our work highlights the roles of RNA structure and sequence in defining substrate specificity and regulating RNA-modifying enzymes.


  • Organizational Affiliation
    • Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 113.2 kDa 
  • Atom Count: 6,217 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 858 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 1

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RNA cytosine C(5)-methyltransferase NSUN2782Homo sapiensMutation(s): 1 
Gene Names: NSUN2SAKITRM4
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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08J23
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
tRNA Lys(TTT)76Homo sapiens
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH

Query on SAH



Download:Ideal Coordinates CCD File
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM122960
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA258589
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesR01ES038329
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM131963
Welch FoundationUnited StatesI-2115-20220331
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP210041
American Cancer SocietyUnited StatesPF-24-1308804-01-RMC
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170644

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release
  • Version 1.1: 2026-06-10
    Changes: Data collection, Database references