[English] 日本語
Yorodumi
- EMDB-63834: Cryo-EM structure of spMETTL16 in complex with U6 snRNA and SAM -

+
Open data


ID or keywords:

Loading...

-
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: To Be Published
Title: Structures and mechanisms of U6 snRNA m6A modification by METTL16
Authors: Ju J / Tomita K
History
DepositionMar 19, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_63834.png

Downloads & links

-
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
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

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 °

-
Supplemental data

-
Mask #1

Fileemd_63834_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_63834_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_63834_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
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

-
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

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

-
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

+
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)

-
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

+
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