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- EMDB-68140: Cryo-EM structure of NSUN2-pre-tRNALeu-SAM -

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Basic information

Entry
Database: EMDB / ID: EMD-68140
TitleCryo-EM structure of NSUN2-pre-tRNALeu-SAM
Map dataCryo-EM structure of NSUN2-pre-tRNAleu-SAM
Sample
  • Complex: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: pre-tRNALeu
  • Ligand: S-ADENOSYLMETHIONINE
KeywordstRNA / m5C RNA methyltransferase / NSUN2 / TRANSFERASE/RNA / TRANSFERASE-RNA 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: 3.3 Å
AuthorsHu Q / Yang W / Li S / Zhang K
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Sci China Life Sci / Year: 2026
Title: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2.
Authors: Qian Hu / Wen Yang / Yunyun Yu / Ran Yi / Yutong Zhang / Leyuan Duan / Fudong Li / Kaiming Zhang / Qingguo Gong / Shanshan Li /
Abstract: The human RNA mC methyltransferase NSUN2 catalyzes site-specific cytosine methylation across diverse RNA substrates and thereby regulates a wide range of biological and physiological processes. ...The human RNA mC methyltransferase NSUN2 catalyzes site-specific cytosine methylation across diverse RNA substrates and thereby regulates a wide range of biological and physiological processes. However, the molecular basis by which NSUN2 achieves broad substrate recognition while maintaining catalytic specificity has remained unclear. Here, we determine structures of human NSUN2 in both substrate-free and substrate-bound states using X-ray crystallography and cryo-electron microscopy. Structures of NSUN2 in complex with multiple tRNA substrates reveal a structure-first, sequence-tolerant strategy in which NSUN2 actively remodels tRNA architecture, exposing the buried target cytosine and positioning it within the catalytic pocket for methyl transfer. This recognition strategy enables NSUN2 to accommodate diverse tRNA substrates through a largely conserved interaction interface. Together, our findings define the molecular principles underlying NSUN2-mediated RNA mC modification.
History
DepositionJan 5, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68140.png

Downloads & links

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Map

FileDownload / File: emd_68140.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of NSUN2-pre-tRNAleu-SAM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 256 pix.
= 248.576 Å		0.97 Å/pix.
x 256 pix.
= 248.576 Å		0.97 Å/pix.
x 256 pix.
= 248.576 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.971 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.054054458 - 0.14969003
Average (Standard dev.)-0.00009146247 (±0.0041125263)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 248.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of NSUN2-pre-tRNAleu-SAM

Fileemd_68140_additional_1.map
AnnotationCryo-EM structure of NSUN2-pre-tRNAleu-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of NSUN2-pre-tRNAleu-SAM

Fileemd_68140_half_map_1.map
AnnotationCryo-EM structure of NSUN2-pre-tRNAleu-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of NSUN2-pre-tRNAleu-SAM

Fileemd_68140_half_map_2.map
AnnotationCryo-EM structure of NSUN2-pre-tRNAleu-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure-driven RNA remodeling underlies broad substrate recogni...

EntireName: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2
Components
  • Complex: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: pre-tRNALeu
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Structure-driven RNA remodeling underlies broad substrate recogni...

SupramoleculeName: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123 KDa

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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: 86.557695 KDa
Recombinant expressionOrganism: Escherichia (bacteria)
SequenceString: MGRRSRGRRL QQQQRPEDAE DGAEGGGKRG EAGWEGGYPE IVKENKLFEH YYQELKIVPE GEWGQFMDAL REPLPATLRI TGYKSHAKE ILHCLKNKYF KELEDLEVDG QKVEVPQPLS WYPEELAWHT NLSRKILRKS PHLEKFHQFL VSETESGNIS R QEAVSMIP ...String:
MGRRSRGRRL QQQQRPEDAE DGAEGGGKRG EAGWEGGYPE IVKENKLFEH YYQELKIVPE GEWGQFMDAL REPLPATLRI TGYKSHAKE ILHCLKNKYF KELEDLEVDG QKVEVPQPLS WYPEELAWHT NLSRKILRKS PHLEKFHQFL VSETESGNIS R QEAVSMIP PLLLNVRPHH KILDMCAAPG SKTTQLIEML HADMNVPFPE GFVIANDVDN KRCYLLVHQA KRLSSPCIMV VN HDASSIP RLQIDVDGRK EILFYDRILC DVPASGDGTM RKNIDVWKKW TTLNSLQLHG LQLRIATRGA EQLAEGGRMV YST CSLNPI EDEAVIASLL EKSEGALELA DVSNELPGLK WMPGITQWKV MTKDGQWFTD WDAVPHSRHT QIRPTMFPPK DPEK LQAMH LERCLRILPH HQNTGGFFVA VLVKKSSMPW NKRQPKLQGK SAETRESTQL SPADLTEGKP TDPSKLESPS FTGTG DTEI AHATEDLENN GSKKDGVCGP PPSKKMKLFG FKEDPFVFIP EDDPLFPPIE KFYALDPSFP RMNLLTRTTE GKKRQL YMV SKELRNVLLN NSEKMKVINT GIKVWCRNNS GEEFDCAFRL AQEGIYTLYP FINSRIITVS MEDVKILLTQ ENPFFRK LS SETYSQAKDL AKGSIVLKYE PDSANPDALQ CPIVLCGWRG KASIRTFVPK NERLHYLRMM GLEVLGEKKK EGVILTNE S AASTGQPDND VTEGQRAGEP NSPDAEEANS PDVTAGCDPA GVHPPR

UniProtKB: RNA cytosine C(5)-methyltransferase NSUN2

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Macromolecule #2: pre-tRNALeu

MacromoleculeName: pre-tRNALeu / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.429973 KDa
SequenceString:
GGUCAGGAUG GCCGAGUGGU CUAAGGCGCC AGACUCAAGG UAAGCACCUU GCCUCCGGGC UUUCUGGUCU CCGGAUGGAG GCGUGGGUU CGAAUCCCAC UUCUGACACC A

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Macromolecule #3: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 112021
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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