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- EMDB-73778: CryoEM structure of human NSUN2(C271A) with SAH cross-linked to t... -

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Basic information

Entry
Database: EMDB / ID: EMD-73778
TitleCryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (D-arm conformation)
Map data
Sample
  • Complex: NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: tRNA Lys(TTT)
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
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: 3.0 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 m5C methyltransferase NSUN2
Authors: Canepa J / Ruiz-Arroyo VM / Schlamowitz N / Nam Y
History
DepositionNov 5, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73778.png

Downloads & links

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Map

FileDownload / File: emd_73778.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-0.104831725 - 0.24656045
Average (Standard dev.)0.00015195024 (±0.006026363)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions252252252
Spacing252252252
CellA=B=C: 247.968 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_73778_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73778_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73778_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH

EntireName: NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH
Components
  • Complex: NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH
    • Protein or peptide: RNA cytosine C(5)-methyltransferase NSUN2
    • RNA: tRNA Lys(TTT)
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH

SupramoleculeName: NSUN2(C271A) and tRNA Lys(TTT) adduct with SAH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: 88.382617 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 DRILCDVPAS 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

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Macromolecule #2: tRNA Lys(TTT)

MacromoleculeName: tRNA Lys(TTT) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.433492 KDa
SequenceString:
GCCUGGAUAG CUCAGUUGGU AGAACAUCAG ACUUUUAAUC UGACGGUG(A1CZ2)A GGGUUCAAGU CCCUGUUCAG GCGC CA

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Macromolecule #3: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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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

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
DetailsThis sample was monodisperse.

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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: 6704 / 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

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Image processing

Particle selectionNumber selected: 738000
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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 239000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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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-9z2u:
CryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(TTT) (D-arm conformation)

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