[English] 日本語
Yorodumi
- EMDB-33137: The Tet-S2 state with a pseudoknotted 4-way junction of wild-type... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33137
TitleThe Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Map data
Sample
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE
KeywordsRNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLuo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y ...Luo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
Funding support China, Poland, European Union, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
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
Polish National Science Centre2017/26/A/NZ1/01083 Poland
Polish National Science Centre2021/43/D/NZ1/03360 Poland
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Nat Catal / Year: 2023
Title: Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing
Authors: Luo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
History
DepositionMar 26, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33137.png

Downloads & links

-
Map

FileDownload / File: emd_33137.map.gz / Format: CCP4 / Size: 42.9 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 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 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: 0.01
Minimum - Maximum-0.06713716 - 0.21414272
Average (Standard dev.)0.0005459729 (±0.005308185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 190.40001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_33137_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33137_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Co-transcriptional folded wild-type Tetrahymena group I intron wi...

EntireName: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Components
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE

-
Supramolecule #1: Co-transcriptional folded wild-type Tetrahymena group I intron wi...

SupramoleculeName: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

-
Macromolecule #1: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...

MacromoleculeName: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 140.071703 KDa
SequenceString: AUAGCAAUAU UUACCUUUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGG CAAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU G GCCUUGCA ...String:
AUAGCAAUAU UUACCUUUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGG CAAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU G GCCUUGCA AAGGGUAUGG UAAUAAGCUG ACGGACAUGG UCCUAACCAC GCAGCCAAGU CCUAAGUCAA CAGAUCUUCU GU UGAUAUG GAUGCAGUUC ACAGACUAAA UGUCGGUCGG GGAAGAUGUA UUCUUCUCAU AAGAUAUAGU CGGACCUCUC CUU AAUGGG AGCUAGCGGA UGAAGUGAUG CAACACUGGA GCCGCUGGGA ACUAAUUUGU AUGCGAAAGU AUAUUGAUUA GUUU UGGAG UACUCGUAAG GUAGCCAAAU GCCUCGUCA

GENBANK: GENBANK: X54512.1

-
Macromolecule #2: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...

MacromoleculeName: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 8.014804 KDa
SequenceString:
ACGGCGGGAG UAACUAUGAC UCUCU

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #4: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00068 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 79.3 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-15 / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 4188150
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ez0

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 494563
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)

-
Atomic model buiding 1

Initial modelPDB ID:

7ez0


Chain - Chain ID: N / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7xd6:
The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon

+
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