[English] 日本語
Yorodumi
- EMDB-38175: Cte-Branch Product, Mg, post -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38175
TitleCte-Branch Product, Mg, post
Map data
Sample
  • Organelle or cellular component: Cte-Branch Product
    • RNA: RNA (808-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsCP group ii intron / Cte / back-splicing / circular RNA / cryo-EM / SPLICING / RNA
Biological speciesComamonas testosteroni KF-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLing XB / Ma JB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC 31971130 China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structures of a natural circularly permuted group II intron reveal mechanisms of branching and backsplicing.
Authors: Xiaobin Ling / Yuqi Yao / Jinbiao Ma /
Abstract: Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA ...Circularly permuted (CP) group II introns, identified in various bacteria phyla, swap domains D5 and D6 near the 5' end and have reversed splice sites (SSs), leading to backsplicing and circular RNA formation. In this study, we present multiple high-resolution cryo-electron microscopy structures of a natural CP group II intron from Comamonas testosteroni KF-1 (Cte 1), elucidating the molecular mechanisms of branching and backsplicing. During branching, the 5' SS is positioned by an auxiliary sequence (AUX)-enhanced interaction between the exon-binding site and intron-binding site (IBS) and stacks on the branch-site adenosine within D6, allowing the attacking 2'-OH group to coordinate with a metal ion in the active center. In backsplicing, the 3' SS is aligned with the branching step, leaving IBS in the active center, stabilized by base pairing with the AUX, which enables the free 3'-end hydroxyl group to directly attack the scissile phosphate of 3' SS. Furthermore, a groove in Cte 1 may stabilize the circular RNA. These findings highlight a conserved catalytic mechanism for canonical group II introns, albeit facilitated by the versatile AUX, opening avenues for designing potent ribozymes producing circular RNAs.
History
DepositionNov 30, 2023-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38175.png

Downloads & links

-
Map

FileDownload / File: emd_38175.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.06
Minimum - Maximum-0.9414894 - 34.064160000000001
Average (Standard dev.)0.027345661 (±0.72221893)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_38175_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38175_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cte-Branch Product

EntireName: Cte-Branch Product
Components
  • Organelle or cellular component: Cte-Branch Product
    • RNA: RNA (808-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

-
Supramolecule #1: Cte-Branch Product

SupramoleculeName: Cte-Branch Product / type: organelle_or_cellular_component / 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: 262.367094 KDa
SequenceString: GCCGGGGCGC CACCCCGGAA GUGAUGCGAG UCGCAACUCG CAUCACAAGC AAACGCUGUA GCCGCGUGCC UCUAAUAGGG CUGGCGCGG UUGCGAAGGG CGCUGGUGAG UGCAACUCUC ACCUUCGACC CAAUCCAUCU UGCGGCUCAA CCCCGCAAGA U CAUCGCCA ...String:
GCCGGGGCGC CACCCCGGAA GUGAUGCGAG UCGCAACUCG 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

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 13 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 13 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 5 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 851556
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
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