[English] 日本語
Yorodumi
- EMDB-73776: CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73776
TitleCryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)
Map data
Sample
  • Complex: NSUN2 and tRNA Lys(CTT) with SFG
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: tRNA Lys(CTT)
  • Ligand: SINEFUNGIN
KeywordsTransferase / Methyltransferase / tRNA / Complex
Function / homology
Function and homology information


tRNA (cytosine34-C5)-methyltransferase / meiotic cell cycle checkpoint signaling / tRNA (cytidine-N5)-methyltransferase activity / tRNA stabilization / mRNA (cytidine-5-)-methyltransferase activity / regulation of mRNA export from nucleus / tRNA modification in the nucleus and cytosol / chromatoid body / hair follicle maturation / tRNA modification ...tRNA (cytosine34-C5)-methyltransferase / meiotic cell cycle checkpoint signaling / tRNA (cytidine-N5)-methyltransferase activity / tRNA stabilization / mRNA (cytidine-5-)-methyltransferase activity / regulation of mRNA export from nucleus / tRNA modification in the nucleus and cytosol / chromatoid body / hair follicle maturation / tRNA modification / tRNA methylation / regulation of stem cell differentiation / spermatid development / Transferases; Transferring one-carbon groups; Methyltransferases / spindle / mRNA processing / in utero embryonic development / tRNA binding / cell division / nucleolus / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
tRNA (C5-cytosine) methyltransferase, NCL1 / : / : / NSUN2 Pre-PUA domain / NSUN2 PUA domain / SAM-dependent methyltransferase RsmB/NOP2-type / RNA (C5-cytosine) methyltransferase / : / 16S rRNA methyltransferase RsmB/F / SAM-dependent MTase RsmB/NOP-type domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
RNA cytosine C(5)-methyltransferase NSUN2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsCanepa J / Ruiz-Arroyo VM / Nam Y
Funding support United States, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122960 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA258589 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R01ES038329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM131963 United States
Welch FoundationI-2115-20220331 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP210041 United States
American Cancer SocietyPF-24-1308804-01-RMC United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP170644 United States
CitationJournal: Nature / Year: 2026
Title: Substrate selectivity of the human RNA mC methyltransferase NSUN2.
Authors: Jacob Canepa / Victor M Ruiz-Arroyo / Netanya S Schlamowitz / Yunsun Nam /
Abstract: Specific deposition of RNA modifications is important for regulating gene expression. 5-Methylcytosine (mC) is a common epitranscriptomic modification, and NSUN2 is a key enzyme responsible for mC ...Specific deposition of RNA modifications is important for regulating gene expression. 5-Methylcytosine (mC) is a common epitranscriptomic modification, and NSUN2 is a key enzyme responsible for mC methylation of various types of RNA. Dysregulation of NSUN2 is associated with numerous diseases, including cancers and neurological disorders. 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 mC 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.
History
DepositionNov 5, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73776.png

Downloads & links

-
Map

FileDownload / File: emd_73776.map.gz / Format: CCP4 / Size: 61 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 252 pix.
= 247.968 Å		0.98 Å/pix.
x 252 pix.
= 247.968 Å		0.98 Å/pix.
x 252 pix.
= 247.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.984 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.09992049 - 0.21082708
Average (Standard dev.)0.00049110706 (±0.0054883254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 247.96799 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_73776_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_73776_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73776_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NSUN2 and tRNA Lys(CTT) with SFG

EntireName: NSUN2 and tRNA Lys(CTT) with SFG
Components
  • Complex: NSUN2 and tRNA Lys(CTT) with SFG
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: tRNA Lys(CTT)
  • Ligand: SINEFUNGIN

-
Supramolecule #1: NSUN2 and tRNA Lys(CTT) with SFG

SupramoleculeName: NSUN2 and tRNA Lys(CTT) with SFG / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: RNA cytosine C(5)-methyltransferase NSUN2

MacromoleculeName: RNA cytosine C(5)-methyltransferase NSUN2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.41468 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHENL YFQGSGGRRS RGRRLQQQQR PEDAEDGAEG GGKRGEAGWE GGYPEIVKEN KLFEHYYQEL KIVPEGEWGQ FMDALREPL PATLRITGYK SHAKEILHCL KNKYFKELED LEVDGQKVEV PQPLSWYPEE LAWHTNLSRK ILRKSPHLEK F HQFLVSET ...String:
MHHHHHHENL YFQGSGGRRS RGRRLQQQQR PEDAEDGAEG GGKRGEAGWE GGYPEIVKEN KLFEHYYQEL KIVPEGEWGQ FMDALREPL PATLRITGYK SHAKEILHCL KNKYFKELED LEVDGQKVEV PQPLSWYPEE LAWHTNLSRK ILRKSPHLEK F HQFLVSET ESGNISRQEA VSMIPPLLLN VRPHHKILDM CAAPGSKTTQ LIEMLHADMN VPFPEGFVIA NDVDNKRCYL LV HQAKRLS SPCIMVVNHD ASSIPRLQID VDGRKEILFY DRILCDVPCS GDGTMRKNID VWKKWTTLNS LQLHGLQLRI ATR GAEQLA EGGRMVYSTC SLNPIEDEAV IASLLEKSEG ALELADVSNE LPGLKWMPGI TQWKVMTKDG QWFTDWDAVP HSRH TQIRP TMFPPKDPEK LQAMHLERCL RILPHHQNTG GFFVAVLVKK SSMPWNKRQP KLQGKSAETR ESTQLSPADL TEGKP TDPS KLESPSFTGT GDTEIAHATE DLENNGSKKD GVCGPPPSKK MKLFGFKEDP FVFIPEDDPL FPPIEKFYAL DPSFPR MNL LTRTTEGKKR QLYMVSKELR NVLLNNSEKM KVINTGIKVW CRNNSGEEFD CAFRLAQEGI YTLYPFINSR IITVSME DV KILLTQENPF FRKLSSETYS QAKDLAKGSI VLKYEPDSAN PDALQCPIVL CGWRGKASIR TFVPKNERLH YLRMMGLE V LGEKKKEGVI LTNESAASTG QPDNDVTEGQ RAGEPNSPDA EEANSPDVTA GCDPAGVHPP R

UniProtKB: RNA cytosine C(5)-methyltransferase NSUN2

-
Macromolecule #2: tRNA Lys(CTT)

MacromoleculeName: tRNA Lys(CTT) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.492529 KDa
SequenceString:
GCCCGGCUAG CUCAGUCGGU AGAGCAUGGG ACUCUUAAUC CCAGGGUCGU GGGUUCGAGC CCCACGUUGG GCGCCA

-
Macromolecule #3: SINEFUNGIN

MacromoleculeName: SINEFUNGIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: SFG
Molecular weightTheoretical: 381.387 Da
Chemical component information

ChemComp-SFG:
SINEFUNGIN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.02 M(HOCH2)3CNH2Tris
0.1 MNaClSodium Chloride
0.002 MMgCl2Magnesium Chloride
0.005 M(CH(OH)CH2SH)2Dithiothreitol
0.02 % (w/v)H(C2H4O)nO(C6H4)C9H19NP40
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8495 / Average exposure time: 3.1 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 669000
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio from cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1-v4

chain_id: A, residue_range: 36-706, source_name: AlphaFold, initial_model_type: in silico model

1fir

chain_id: A, residue_range: 1-73, source_name: PDB, initial_model_type: experimental model
Output model

PDB-9z2r:
CryoEM structure of human NSUN2 with tRNA Lys(CTT) and SFG (D-arm conformation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more