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- PDB-9z2n: CryoEM structure of human NSUN2(C271A) with SAH cross-linked to t... -

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Basic information

Entry
Database: PDB / ID: 9z2n
TitleCryoEM structure of human NSUN2(C271A) with SAH cross-linked to tRNA Lys(CTT) (D-arm conformation)
Components
  • RNA cytosine C(5)-methyltransferase NSUN2
  • tRNA Lys(CTT)
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
S-ADENOSYL-L-HOMOCYSTEINE / : / RNA / RNA (> 10) / RNA cytosine C(5)-methyltransferase NSUN2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsCanepa, J. / Ruiz-Arroyo, V.M. / Nam, Y.
Funding support United States, 8items
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, V.M. / Schlamowitz, N. / Nam, Y.
History
DepositionNov 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA cytosine C(5)-methyltransferase NSUN2
B: tRNA Lys(CTT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2763
Polymers112,8912
Non-polymers3841
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein RNA cytosine C(5)-methyltransferase NSUN2 / Myc-induced SUN domain-containing protein / Misu / NOL1/NOP2/Sun domain family member 2 / Substrate ...Myc-induced SUN domain-containing protein / Misu / NOL1/NOP2/Sun domain family member 2 / Substrate of AIM1/Aurora kinase B / mRNA cytosine C(5)-methyltransferase / tRNA cytosine C(5)-methyltransferase / tRNA methyltransferase 4 homolog / hTrm4


Mass: 88382.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSUN2, SAKI, TRM4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08J23, Transferases; Transferring one-carbon groups; Methyltransferases, tRNA (cytosine34-C5)-methyltransferase
#2: RNA chain tRNA Lys(CTT)


Mass: 24508.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 175760
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NSUN2(C271A) and tRNA Lys(CTT) adduct with SAH / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.02 MTris(HOCH2)3CNH21
20.1 MSodium ChlorideNaCl1
30.002 MMagnesium ChlorideMgCl21
40.005 MDithiothreitol(CH(OH)CH2SH)21
50.02 % (w/v)NP40H(C2H4O)nO(C6H4)C9H191
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8928
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEM4.1image acquisition
4cryoSPARCCTF correction
7Coot0.9.8.7model fitting
9PHENIX1.21.1_5286model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 874000
3D reconstructionResolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243000 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Chain-ID: A

IDPDB-IDPdb chain-IDAccession codeChain residue rangeInitial refinement model-IDSource nameTypePdb chain residue range
1AF-Q08J23-F1-v436-7061AlphaFoldin silico model
21FIR

1fir

A1FIR1-732PDBexperimental model1-73
RefinementHighest resolution: 2.57 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026788
ELECTRON MICROSCOPYf_angle_d0.4769560
ELECTRON MICROSCOPYf_dihedral_angle_d17.1733051
ELECTRON MICROSCOPYf_chiral_restr0.0381114
ELECTRON MICROSCOPYf_plane_restr0.004944

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