[English] 日本語
Yorodumi
- EMDB-38647: Comamonas testosteroni KF-1 circularly permuted group II intron 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38647
TitleComamonas testosteroni KF-1 circularly permuted group II intron 1S state
Map data
Sample
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron 1S state
    • RNA: RNA (808-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
KeywordsCryoEM / Ribozyme / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsWang L / Xie JH / Zhang C / Zou J / Huang ZR / Shang ST / Chen XY / Yang Y / Liu J / Dong HH ...Wang L / Xie JH / Zhang C / Zou J / Huang ZR / Shang ST / Chen XY / Yang Y / Liu J / Dong HH / Huang DM / Su ZM
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of circularly permuted group II intron self-splicing.
Authors: Liu Wang / Jiahao Xie / Chong Zhang / Jian Zou / Zirui Huang / Sitong Shang / Xingyu Chen / Yang Yang / Jianquan Liu / Haohao Dong / Dingming Huang / Zhaoming Su /
Abstract: Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. ...Circularly permuted group II introns (CP introns) consist of rearranged structural domains separated by two tethered exons, generating branched introns and circular exons via back-splicing. Structural and mechanistic understanding of circular RNA (circRNA) generation by CP introns remains elusive. We resolve cryo-electron microscopy structures of a natural CP intron in different states during back-splicing at a resolution of 2.5-2.9 Å. Domain 6 (D6) undergoes a conformational change of 65° after branching, to facilitate 3'-exon recognition and circularization. Previously unseen tertiary interactions compact the catalytic triad and D6 for splicing without protein, whereas a metal ion, M, is observed to stabilize the 5'-exon during splicing. While these unique features were not observed in canonical group II introns and spliceosomes, they are common in CP introns, as demonstrated by the cryo-EM structure of another CP intron discovered by comparative genomics analysis. Our results elucidate the mechanism of CP intron back-splicing dynamics, with potential applications in circRNA research and therapeutics.
History
DepositionJan 11, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38647.png

Downloads & links

-
Map

FileDownload / File: emd_38647.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.39721072 - 0.78006023
Average (Standard dev.)0.00085219333 (±0.013415014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_38647_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38647_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Comamonas testosteroni KF-1 circularly permuted group II intron 1...

EntireName: Comamonas testosteroni KF-1 circularly permuted group II intron 1S state
Components
  • Complex: Comamonas testosteroni KF-1 circularly permuted group II intron 1S state
    • RNA: RNA (808-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Comamonas testosteroni KF-1 circularly permuted group II intron 1...

SupramoleculeName: Comamonas testosteroni KF-1 circularly permuted group II intron 1S state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)

-
Macromolecule #1: RNA (808-MER)

MacromoleculeName: RNA (808-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Comamonas testosteroni KF-1 (bacteria)
Molecular weightTheoretical: 262.327062 KDa
SequenceString: CCGGGGCGCC ACCCCGGAAG UGAUGCGAGU CGCCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA ...String:
CCGGGGCGCC ACCCCGGAAG UGAUGCGAGU CGCCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA GACCGCUGGC GGCGUACUGA GUGACAAACG AGGCAAAACC AAAUUGAAGU UGGGCGACCG UGAAACGGCG CU GGGCAGG AAAUGGCCCA GUGACCUGGU CAAUGGUGAA AGUCGGUGAA AGACCGACCG GUGGGGCGUA UCGAAAGAGC GCA ACACCU GCCGCACAGG AUGGCUUCUG AGGUACCGGU GACGGUACAG AACGCGGAGG GGAAACCUGG AAGCGAGGGC ACCU CGGGA AACCGGGGGU CGAUGCAUAG CUCAAACCUG UAACGGCACC AGUGGAGGGU GCUGUGCGGA GCAACGUGGA GCCAC AGGC AUGAAGCCGU GGUUCGUAGU CGAUGAGACA AGCGGUGAGU AAGGGAAGGG CUGCGAACAU CGCCUCCCCG AAAUCC AAG GAAAGCCGAA AGGCUAGCCG CUUUGUUGAG ACAGUGGCGC CACGUUGCGC AUUAGCCGUG ACCUAAACGG GGAACCU CU UGGCCGUACC GACUCGGGUG GCACCGGUCG GGCUCGAUGG CUCAAGAGGG GGAGAUGUGA UGAUUAGGGU UUGACCCG U GAUGCGAUAC GACCGAAGCA UCCGGGGAGC UGUCUGACGA AGAGUCGGCA GCAGUGGGUU UGGCGACCCG CUCCGAAAG UCGCAAGC

GENBANK: GENBANK: CP140157.1

-
Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 5 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 32 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46777
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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