[English] 日本語
Yorodumi
- EMDB-49525: Cryo-EM structure of the trimeric SenDRT9 RT-ncRNA complex (GST f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49525
TitleCryo-EM structure of the trimeric SenDRT9 RT-ncRNA complex (GST fusion)
Map data
Sample
  • Complex: Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric complex fused to GST
    • Protein or peptide: Sen DRT9 reverse transcriptase
    • RNA: RNA (141-MER)
KeywordsDRT9 / Complex / IMMUNE SYSTEM
Biological speciesSalmonella enterica (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBurman N / Pandey S / Wiedenheft B / Sternberg SH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867 United States
National Science Foundation (NSF, United States)2239685 United States
CitationJournal: Nature / Year: 2025
Title: Protein-primed homopolymer synthesis by an antiviral reverse transcriptase.
Authors: Stephen Tang / Rimantė Žedaveinytė / Nathaniel Burman / Shishir Pandey / Josephine L Ramirez / Louie M Kulber / Tanner Wiegand / Royce A Wilkinson / Yanzhe Ma / Dennis J Zhang / George D ...Authors: Stephen Tang / Rimantė Žedaveinytė / Nathaniel Burman / Shishir Pandey / Josephine L Ramirez / Louie M Kulber / Tanner Wiegand / Royce A Wilkinson / Yanzhe Ma / Dennis J Zhang / George D Lampe / Mirela Berisa / Marko Jovanovic / Blake Wiedenheft / Samuel H Sternberg /
Abstract: Bacteria defend themselves from viral predation using diverse immune systems, many of which target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide an ...Bacteria defend themselves from viral predation using diverse immune systems, many of which target foreign DNA for degradation. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this strategy by leveraging DNA synthesis instead. We and others recently showed that DRT2 systems use an RNA template to assemble a de novo gene that encodes an antiviral effector protein, Neo. It remains unknown whether similar mechanisms of defense are employed by other related DRT families. Focusing on DRT9, here we uncover an unprecedented mechanism of DNA homopolymer synthesis. Viral infection triggers polydeoxyadenylate (poly-dA) accumulation in the cell, driving abortive infection and population-level immunity. Cryo-EM structures reveal how a noncoding RNA serves as both a structural scaffold and reverse transcription template to direct hexameric complex assembly and poly-dA synthesis. Remarkably, biochemical and functional experiments identify tyrosine residues within the reverse transcriptase itself that likely prime DNA synthesis, leading to the formation of high-molecular weight protein-DNA covalent adducts. Synthesis of poly-dA by DRT9 in vivo is regulated by the competing activities of phage-encoded triggers and host-encoded silencers. Collectively, our work unveils a novel nucleic acid-driven defense system that expands the paradigm of bacterial immunity and broadens the known functions of reverse transcriptases.
History
DepositionMar 3, 2025-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49525.png

Downloads & links

-
Map

FileDownload / File: emd_49525.map.gz / Format: CCP4 / Size: 465.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 496 pix.
= 449.426 Å		0.91 Å/pix.
x 496 pix.
= 449.426 Å		0.91 Å/pix.
x 496 pix.
= 449.426 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.29225993 - 0.7720487
Average (Standard dev.)-0.00013133464 (±0.011392598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions496496496
Spacing496496496
CellA=B=C: 449.4256 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_49525_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49525_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric comple...

EntireName: Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric complex fused to GST
Components
  • Complex: Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric complex fused to GST
    • Protein or peptide: Sen DRT9 reverse transcriptase
    • RNA: RNA (141-MER)

-
Supramolecule #1: Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric comple...

SupramoleculeName: Cryo-EM structure of the SenDRT9-encoded RT-ncRNA trimeric complex fused to GST
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica (bacteria)

-
Macromolecule #1: Sen DRT9 reverse transcriptase

MacromoleculeName: Sen DRT9 reverse transcriptase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 58.318961 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKLEQQIQRV ILEEAKALIK DYHEYHNRVH LESVRNKKRL GDSAPDKKIH RPNYWSFDKK FDPFYVKSNY KSIARSIANK IENRTYLPN EPFTKDVPKP DGGIRKVSIY QIPDAAISKL FFNRLLAKNR HRFSSFSYAY RNDRNVHFAI QDISVDLKKN E RTFLAEFD ...String:
MKLEQQIQRV ILEEAKALIK DYHEYHNRVH LESVRNKKRL GDSAPDKKIH RPNYWSFDKK FDPFYVKSNY KSIARSIANK IENRTYLPN EPFTKDVPKP DGGIRKVSIY QIPDAAISKL FFNRLLAKNR HRFSSFSYAY RNDRNVHFAI QDISVDLKKN E RTFLAEFD FSDFFGSISH SFLNEQFNEN GFYISPEEKF IIRSFLRERK VGIPQGTSIS LFLANLTCWK LDQDLEREGV KF SRYADDT IIWSQEYSKI CNAFNIITNF SKSAGIKINP KKSEGISLLT KKGLPSEITS KNNLDFLGYT LSVENVSIKE KSV KKIKKQ ISYILYRNLI QPLKKTSLAG QTIPANDRDK NFLIAICEIR RYMYGGLSKS QIKDYLSGRS NRLYFKGIMS FYPL VNDVE QLKQLDGWIV SVIYRALKLR CQLLSKWGYN RSHNFPFILD REDIVDKCSK KTIAGRKLFE IPSFLLIHKA LQKGL QESG IEKIMNPQSL NYDYE

-
Macromolecule #2: RNA (141-MER)

MacromoleculeName: RNA (141-MER) / type: rna / ID: 2 / Number of copies: 3
Source (natural)Organism: Salmonella enterica (bacteria)
Molecular weightTheoretical: 45.359656 KDa
SequenceString:
CUCAUAGGGA UAACGGUGUG GCCUUCUACC UGUUAGAAAU AAUGGGUCUU CAGUUGUAAU UCGUUGCAAC UGACGGGGGG GUGGUGUCA AAGCCGUUUC AACCAAGUGG UAACUUACUU UUACUUGGGU UUAUACCGUG GA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.6.2) / Software - details: Non-Uniform Refinement / Number images used: 367640
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