[English] 日本語
Yorodumi
- EMDB-45086: Structure of the elongating DRT2 reverse transcriptase in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45086
TitleStructure of the elongating DRT2 reverse transcriptase in complex with its non-coding RNA and dNTPs
Map dataSharpened map of the elongating UG2 reverse transcriptase ribonucleoprotein complex
Sample
  • Complex: UG2 reverse transcriptase ribonucleoprotein complex, elongating state
    • Protein or peptide: Reverse transcriptase/maturase family protein
    • DNA: ccDNA
    • RNA: DRT2 ncRNA
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: POTASSIUM ION
Keywordsreverse transcriptase / rolling circle amplification / phage defense / TRANSFERASE-DNA-RNA complex
Function / homology: / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / RNA-directed DNA polymerase activity / DNA/RNA polymerase superfamily / Reverse transcriptase/maturase family protein
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsWilkinson ME / Zhang F
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Phage-triggered reverse transcription assembles a toxic repetitive gene from a noncoding RNA.
Authors: Max E Wilkinson / David Li / Alex Gao / Rhiannon K Macrae / Feng Zhang /
Abstract: Reverse transcription has frequently been co-opted for cellular functions and in prokaryotes is associated with protection against viral infection, but the underlying mechanisms of defense are ...Reverse transcription has frequently been co-opted for cellular functions and in prokaryotes is associated with protection against viral infection, but the underlying mechanisms of defense are generally unknown. Here, we show that in the DRT2 defense system, the reverse transcriptase binds a neighboring pseudoknotted noncoding RNA. Upon bacteriophage infection, a template region of this RNA is reverse transcribed into an array of tandem repeats that reconstitute a promoter and open reading frame, allowing expression of a toxic repetitive protein and an abortive infection response. Biochemical reconstitution of this activity and cryo-electron microscopy provide a molecular basis for repeat synthesis. Gene synthesis from a noncoding RNA is a previously unknown mode of genetic regulation in prokaryotes.
History
DepositionMay 25, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_45086.png

Downloads & links

-
Map

FileDownload / File: emd_45086.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the elongating UG2 reverse transcriptase ribonucleoprotein complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 240 pix.
= 212.16 Å		0.88 Å/pix.
x 240 pix.
= 212.16 Å		0.88 Å/pix.
x 240 pix.
= 212.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.884 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.08474546 - 0.13420972
Average (Standard dev.)-0.00014777922 (±0.0037313404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 212.16 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: UG2 RNP with dNTPs refinement, half-map 1

Fileemd_45086_half_map_1.map
AnnotationUG2 RNP with dNTPs refinement, half-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: UG2 RNP with dNTPs refinement, half-map 2

Fileemd_45086_half_map_2.map
AnnotationUG2 RNP with dNTPs refinement, half-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : UG2 reverse transcriptase ribonucleoprotein complex, elongating state

EntireName: UG2 reverse transcriptase ribonucleoprotein complex, elongating state
Components
  • Complex: UG2 reverse transcriptase ribonucleoprotein complex, elongating state
    • Protein or peptide: Reverse transcriptase/maturase family protein
    • DNA: ccDNA
    • RNA: DRT2 ncRNA
  • Ligand: MAGNESIUM ION
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
  • Ligand: POTASSIUM ION

-
Supramolecule #1: UG2 reverse transcriptase ribonucleoprotein complex, elongating state

SupramoleculeName: UG2 reverse transcriptase ribonucleoprotein complex, elongating state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 140 KDa

-
Macromolecule #1: Reverse transcriptase/maturase family protein

MacromoleculeName: Reverse transcriptase/maturase family protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 49.788645 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNDDYPWFR KRGYLHFDEP VSLKKAVKYV SSPEKIIKHS FLPFLSFEVK SFKIKKDKST KQLSKTEKLR PIAYSSHLDS HIYAFYAEY LTGHYELLIQ ENNLHENILA FRSLNKSNIE FAKRAFDTIT EMGECSAVAL DLSGFFDNLD HQILKHQWCK V IGTEALPQ ...String:
MNNDDYPWFR KRGYLHFDEP VSLKKAVKYV SSPEKIIKHS FLPFLSFEVK SFKIKKDKST KQLSKTEKLR PIAYSSHLDS HIYAFYAEY LTGHYELLIQ ENNLHENILA FRSLNKSNIE FAKRAFDTIT EMGECSAVAL DLSGFFDNLD HQILKHQWCK V IGTEALPQ DHFAIYKSIT RYSKVDKNRA YEILGISKNN PKYNRRKICT PVDFRNKIRK NGLIIVNNSQ KGIPQGSPIS AL LSNIYML DFDIEMRDYA QERGGHYYRY CDDMLFIVPT KYNKTLAGDV AQRIKHLKVE LNTKKTEIRD FIYKDSTLVA NMP LQYLGF IFDGSNILLR SSSLARYSER MKRGVRLAKA TMDSKNRIRE NKGEALKALF KKKLYARYSH IGRRNFLTYG YRAA KIMNS KAIKRQLKPL QKRLENEILK

UniProtKB: Reverse transcriptase/maturase family protein

-
Macromolecule #2: ccDNA

MacromoleculeName: ccDNA / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 2.745821 KDa
SequenceString:
(DT)(DA)(DT)(DG)(DC)(DT)(DG)(DT)(DA)

-
Macromolecule #3: DRT2 ncRNA

MacromoleculeName: DRT2 ncRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Klebsiella pneumoniae (bacteria)
Molecular weightTheoretical: 90.951438 KDa
SequenceString: GGCCCUAAAC AAAGGUUUAG GGGUAUUGUA CAGGUUGUCA AGCCUCCCAC AGGUCUUGGU GAAACCAAUC ACUGUGACGA CGGUAAGCA ACACUUGGAU GAUAUUCAUA AUUGACUCCA CGCUACUGAU UACAUUAUAC AGCAUAUCUA ACAUUUGCGG C GAGGUUCA ...String:
GGCCCUAAAC AAAGGUUUAG GGGUAUUGUA CAGGUUGUCA AGCCUCCCAC AGGUCUUGGU GAAACCAAUC ACUGUGACGA CGGUAAGCA ACACUUGGAU GAUAUUCAUA AUUGACUCCA CGCUACUGAU UACAUUAUAC AGCAUAUCUA ACAUUUGCGG C GAGGUUCA CAAUUUGUAU UUAGGUACUG AUUGUGGAUG AGAAGGUUGG AGAAAGACCA CUUGGUUAAG CCGGAGGAUG UG UCCUAGA AUUGUCGCUA UUCUGUCAUC CUCCGGUUUU GCUAAU

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

-
Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 18453 / Average electron dose: 40.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3313207
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 136601
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