[English] 日本語
Yorodumi
- EMDB-68111: Cryo-EM structure of NSUN2-tRNAlys-SAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68111
TitleCryo-EM structure of NSUN2-tRNAlys-SAM
Map dataCryo-EM structure of NSUN2-tRNAlys-SAM
Sample
  • Complex: Structure-driven RNA remodeling underlies broad substrate recognition by NSUN2
    • Protein or peptide: NSUN2
    • RNA: tRNAlys (77-MER)
  • Ligand: S-ADENOSYLMETHIONINE
KeywordstRNA / m5C RNA methyltransferase / NSUN2 / TRANSFERASE/RNA / TRANSFERASE-RNA complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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 4, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68111.png

Downloads & links

-
Map

FileDownload / File: emd_68111.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of NSUN2-tRNAlys-SAM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.061294988 - 0.13586028
Average (Standard dev.)-0.0000686253 (±0.004228152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Cryo-EM structure of NSUN2-tRNAlys-SAM

Fileemd_68111_additional_1.map
AnnotationCryo-EM structure of NSUN2-tRNAlys-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of NSUN2-tRNAlys-SAM

Fileemd_68111_half_map_1.map
AnnotationCryo-EM structure of NSUN2-tRNAlys-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of NSUN2-tRNAlys-SAM

Fileemd_68111_half_map_2.map
AnnotationCryo-EM structure of NSUN2-tRNAlys-SAM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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: NSUN2
    • RNA: tRNAlys (77-MER)
  • Ligand: S-ADENOSYLMETHIONINE

-
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: 113 KDa

-
Macromolecule #1: NSUN2

MacromoleculeName: NSUN2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
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

-
Macromolecule #2: tRNAlys (77-MER)

MacromoleculeName: tRNAlys (77-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.762656 KDa
SequenceString:
GGCCUGGAUA GCUCAGUUGG UAGAGCAUCA GACUUUUAAU CUGAGGGUCC AGGGUUCAAG UCCCUGUUCA GGCACCA

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 67546
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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