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- EMDB-63834: Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM -

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Basic information

Entry
Database: EMDB / ID: EMD-63834
TitleCryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM
Map dataProcessed by deepEMhancer
Sample
  • Complex: Schizosaccharomyces pombe N6-methyladenosine methyltransferase METTL16 in complex with U6 snRNA and SAM
    • Protein or peptide: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
    • RNA: U6 small nuclear RNA
  • Ligand: S-ADENOSYLMETHIONINE
Keywordsm6A methyltransferase / U6 snRNA / protein-RNA complex / splicing / TRANSFERASE / TRANSFERASE-RNA complex
Function / homology
Function and homology information


snRNA (adenine-N6)-methylation / U6 snRNA m6A methyltransferase / U6 snRNA (adenine-(43)-N(6))-methyltransferase activity / rRNA base methylation / mRNA splicing, via spliceosome / nucleus / cytosol
Similarity search - Function
Methyltransferase METTL16/PsiM / RNA methyltransferase / METTL16/RlmF family / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsJu J / Tomita K
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00368 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structures and mechanisms of U6 snRNA mA modification by METTL16.
Authors: Jue Ju / Kozo Tomita /
Abstract: The N-methyladenosine (mA) modification in U6 snRNA, catalyzed by METTL16 using S-adenosylmethionine (SAM) as the methyl donor, is required for efficient and accurate pre-mRNA splicing. However, the ...The N-methyladenosine (mA) modification in U6 snRNA, catalyzed by METTL16 using S-adenosylmethionine (SAM) as the methyl donor, is required for efficient and accurate pre-mRNA splicing. However, the mechanism by which METTL16 modifies U6 snRNA with mA remains elusive. Here, we present cryo-EM structures of METTL16 in complex with U6 snRNA, providing insights into the METTL16-mediated modification of U6 snRNA with mA. The structures reveal that U6 snRNA is recruited to METTL16 through specific interactions between the C-terminal kinase-associated 1 (KA-1) domain of METTL16 and the internal stem-loop (ISL) of U6 snRNA. Upon SAM binding to the catalytic pocket within the N-terminal methyltransferase domain (MTD), U6 snRNA undergoes a structural rearrangement that positions the target adenine-containing motif at the catalytic site. This conformational change is followed by an additional structural adjustment of U6 snRNA into a productive conformation, bringing the target adenosine closer to SAM within the catalytic pocket and thereby ensuring efficient mA modification. The KA-1 domain functions as a scaffold for initial substrate recognition and facilitates the subsequent dynamic methylation process within the MTD, highlighting the cooperative roles of METTL16 domains for U6 snRNA modification.
History
DepositionMar 19, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63834.png

Downloads & links

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Map

FileDownload / File: emd_63834.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProcessed by deepEMhancer
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å		0.83 Å/pix.
x 324 pix.
= 268.92 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0162
Minimum - Maximum-0.0017824713 - 2.429685
Average (Standard dev.)0.00043148018 (±0.016217584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 268.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63834_msk_1.map
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Half map: #2

Fileemd_63834_half_map_1.map
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Half map: #1

Fileemd_63834_half_map_2.map
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Sample components

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Entire : Schizosaccharomyces pombe N6-methyladenosine methyltransferase ME...

EntireName: Schizosaccharomyces pombe N6-methyladenosine methyltransferase METTL16 in complex with U6 snRNA and SAM
Components
  • Complex: Schizosaccharomyces pombe N6-methyladenosine methyltransferase METTL16 in complex with U6 snRNA and SAM
    • Protein or peptide: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
    • RNA: U6 small nuclear RNA
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: Schizosaccharomyces pombe N6-methyladenosine methyltransferase ME...

SupramoleculeName: Schizosaccharomyces pombe N6-methyladenosine methyltransferase METTL16 in complex with U6 snRNA and SAM
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Macromolecule #1: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase

MacromoleculeName: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase
type: protein_or_peptide / ID: 1
Details: Residues MET A -22 to SER A 0 are expression tags. MET A 1 to PHE A 23 are part of the protein sequence, based on publication (DOI: 10.1038/s41467-021-23457-6).
Number of copies: 1 / Enantiomer: LEVO / EC number: U6 snRNA m6A methyltransferase
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / Strain: ED668
Molecular weightTheoretical: 48.442223 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTDKTDI INFDSLARDY PDLRSFVKNG RIDFWNEDAI RTLGKAILDR DYSLRVEFPE NRLCPMVPN RATYIRYIHD LLSSTSGQKD KKRIIGLDIG TGASCIYPLL GCRMYSYDFV GTEIDKFSFE TAKSNILQNN M ESQIKIVL ...String:
MGSSHHHHHH SSGLVPRGSH MASMTDKTDI INFDSLARDY PDLRSFVKNG RIDFWNEDAI RTLGKAILDR DYSLRVEFPE NRLCPMVPN RATYIRYIHD LLSSTSGQKD KKRIIGLDIG TGASCIYPLL GCRMYSYDFV GTEIDKFSFE TAKSNILQNN M ESQIKIVL RSKQDCLLPD TEGMEEFTFV MCNPPFYEHE EDFINFKQNP PSGVCTGVYH EMVTEGGEVG FANKILTESK KR KGIQWYT CMFGKKSSVP AVVDKLREQN ISNYGIYELA LGKTKRWIIC WSFQAMRPHN ELIRPSSTSL SKYFPHKVLQ NWT LDPELC AQIDDILQKF LDDNKIPWSK KGSVLEISTK SITWSRKARR ISKSQTSVSS LEGQMKCELN VIDNQLQCKW IEGY DYNVY ESFCSALARA LRDNKK

UniProtKB: U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase

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Macromolecule #2: U6 small nuclear RNA

MacromoleculeName: U6 small nuclear RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 31.863982 KDa
SequenceString:
GAUCUUCGGA UCACUUUGGU CAAAUUGAAA CGAUACAGAG AAGAUUAGCA UGGCCCCUGC ACAAGGAUGA CACUGCGACA UUGAGAGAA AACCCAUUUU

GENBANK: GENBANK: 3JB9_N

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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

BufferpH: 7
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4092 pixel / Digitization - Dimensions - Height: 5760 pixel / Number grids imaged: 1 / Number real images: 8497 / Average exposure time: 1.0 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5415176
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 425927
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9u48:
Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM

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