[English] 日本語
Yorodumi
- EMDB-26550: CryoEM Structure of an Group II Intron Retroelement -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26550
TitleCryoEM Structure of an Group II Intron Retroelement
Map dataHoloRNP Full Consensus Map
Sample
  • Complex: Ternary complex of RNA, protein and DNA
    • RNA: E.r IIC Intron
    • Protein or peptide: Group II intron reverse transcriptase/maturase
    • DNA: DNA (37-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: AMMONIUM ION
  • Ligand: water
KeywordsRNA / intron / group II / maturase / splicing / retrotransposition / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity
Similarity search - Function
Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Group II intron reverse transcriptase/maturase
Similarity search - Component
Biological species[Eubacterium] rectale (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsChung K / Xu L
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Structures of a mobile intron retroelement poised to attack its structured DNA target.
Authors: Kevin Chung / Ling Xu / Pengxin Chai / Junhui Peng / Swapnil C Devarkar / Anna Marie Pyle /
Abstract: Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam ...Group II introns are ribozymes that catalyze their self-excision and function as retroelements that invade DNA. As retrotransposons, group II introns form ribonucleoprotein (RNP) complexes that roam the genome, integrating by reversal of forward splicing. Here we show that retrotransposition is achieved by a tertiary complex between a structurally elaborate ribozyme, its protein mobility factor, and a structured DNA substrate. We solved cryo-electron microscopy structures of an intact group IIC intron-maturase retroelement that was poised for integration into a DNA stem-loop motif. By visualizing the RNP before and after DNA targeting, we show that it is primed for attack and fits perfectly with its DNA target. This study reveals design principles of a prototypical retroelement and reinforces the hypothesis that group II introns are ancient elements of genetic diversification.
History
DepositionMar 29, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26550.png

Downloads & links

-
Map

FileDownload / File: emd_26550.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHoloRNP Full Consensus Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.1059777 - 2.0479062
Average (Standard dev.)-0.00018932996 (±0.033899605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

-
Supplemental data

+
Mask #1

Fileemd_26550_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Mask #2

Fileemd_26550_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Left) Map

Fileemd_26550_additional_1.map
AnnotationHoloRNP Focused Refined (Left) Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Right) Map

Fileemd_26550_additional_2.map
AnnotationHoloRNP Focused Refined (Right) Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Composite Map

Fileemd_26550_additional_3.map
AnnotationHoloRNP Composite Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Right) Halm Map A

Fileemd_26550_additional_4.map
AnnotationHoloRNP Focused Refined (Right) Halm Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Left) Halm Map A

Fileemd_26550_additional_5.map
AnnotationHoloRNP Focused Refined (Left) Halm Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Right) Halm Map B

Fileemd_26550_additional_6.map
AnnotationHoloRNP Focused Refined (Right) Halm Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Additional map: HoloRNP Focused Refined (Left) Halm Map B

Fileemd_26550_additional_7.map
AnnotationHoloRNP Focused Refined (Left) Halm Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: HoloRNP Full Consensus Half Map A

Fileemd_26550_half_map_1.map
AnnotationHoloRNP Full Consensus Half Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

+
Half map: HoloRNP Full Consensus Half Map B

Fileemd_26550_half_map_2.map
AnnotationHoloRNP Full Consensus Half Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of RNA, protein and DNA

EntireName: Ternary complex of RNA, protein and DNA
Components
  • Complex: Ternary complex of RNA, protein and DNA
    • RNA: E.r IIC Intron
    • Protein or peptide: Group II intron reverse transcriptase/maturase
    • DNA: DNA (37-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: AMMONIUM ION
  • Ligand: water

-
Supramolecule #1: Ternary complex of RNA, protein and DNA

SupramoleculeName: Ternary complex of RNA, protein and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 260 KDa

-
Macromolecule #1: E.r IIC Intron

MacromoleculeName: E.r IIC Intron / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 206.779859 KDa
SequenceString: GUUUGCGCGC CAUGGGCGCG CUCUAACGGG UGUAAGUCCC GAACAUGCCC AGGUAGUGGG AAAUGUAUAG CCGAACAGCA AGGGUGUCU ACUGUGAGGU GGAAUCUGAA GGAAGCUGUA AGCGAAUCUC UGGUCCGACG GACAGAAAUC GCAUAUAAGG C UAGGCUUC ...String:
GUUUGCGCGC CAUGGGCGCG CUCUAACGGG UGUAAGUCCC GAACAUGCCC AGGUAGUGGG AAAUGUAUAG CCGAACAGCA AGGGUGUCU ACUGUGAGGU GGAAUCUGAA GGAAGCUGUA AGCGAAUCUC UGGUCCGACG GACAGAAAUC GCAUAUAAGG C UAGGCUUC GAGUGAUAAG CUGGCAAAGA ACAGUGAAGU CUAAUAACUA CCACGUUUGU AGAAGCAGAG UAAAUGCGGC GG AUAUAUG GAGAGAAAGA GCGUGCACCU UAAGCGUGGA GGUCUCACAG AGGUUUCAUU AGCCUAGUAA CAACGAACUG UGA GAAGUC AGCCGAGCCC AUAGUAGUGA AGAAGUCUCU GUAAUGGGGA UGGAGCGAAG GGGCGAACAA UCAUUCAGUU UGAG AAUGU CUCGUAUUGC AGAAAUGACA ACAUCUGCCG UAACCAAUCG GGUAAAAGGU GGUCAAAUCA AGCGAGACGG AAAGG AAAG AACGCAUGGA CACAAGUAAU CUAAUUUCGG UUAGAUUACU ACAUCGAAAA GUGUGUUACU UGUUAAGUUG AUUGAA CCG CCGUAUACGG AACCGUACGU ACGGUGGUGU GAGAGGUCGG AAUUUCUCAA UUAAGAGAAA UUCUUCCUAC UCGAU

-
Macromolecule #2: Group II intron reverse transcriptase/maturase

MacromoleculeName: Group II intron reverse transcriptase/maturase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 49.083914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI ...String:
MDTSNLMEQI LSSDNLNRAY LQVVRNKGAE GVDGMKYTEL KEHLAKNGET IKGQLRTRKY KPQPARRVEI PKPDGGVRNL GVPTVTDRF IQQAIAQVLT PIYEEQFHDH SYGFRPNRCA QQAILTALNI MNDGNDWIVD IDLEKFFDTV NHDKLMTLIG R TIKDGDVI SIVRKYLVSG IMIDDEYEDS IVGTPQGGNL SPLLANIMLN ELDKEMEKRG LNFVRYADDC IIMVGSEMSA NR VMRNISR FIEEKLGLKV NMTKSKVDRP SGLKYLGFGF YFDPRAHQFK AKPHAKSVAK FKKRMKELTC RSWGVSNSYK VEK LNQLIR GWINYFKIGS MKTLCKELDS RIRYRLRMCI WKQWKTPQNQ EKNLVKLGID RNTARRVAYT GKRIAYVCNK GAVN VAISN KRLASFGLIS MLDYYIEKCV TC

UniProtKB: Group II intron reverse transcriptase/maturase

-
Macromolecule #3: DNA (37-MER)

MacromoleculeName: DNA (37-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: [Eubacterium] rectale (bacteria)
Molecular weightTheoretical: 11.403316 KDa
SequenceString:
(DG)(DA)(DG)(DA)(DG)(DC)(DA)(DG)(DG)(DG) (DG)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DC)(DC) (DT)(DG)(DC)(DT)(DC)(DT)(DC)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DT)(DG)

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: AMMONIUM ION

MacromoleculeName: AMMONIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: NH4
Molecular weightTheoretical: 18.038 Da
Chemical component information

ChemComp-NH4:
AMMONIUM ION

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 24 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3eoh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 914099
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1)
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