[English] 日本語
Yorodumi
- PDB-9jm0: retron Ec86-effector fiber -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jm0
Titleretron Ec86-effector fiber
Components
  • DNA (85-MER)
  • RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')
  • RNA (82-MER)
  • Retron Ec86 putative ribosyltransferase/DNA-binding protein
  • Retron Ec86 reverse transcriptase
KeywordsRNA BINDING PROTEIN/DNA/RNA / Reverse transcriptase / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / defense response to virus / RNA binding / metal ion binding
Similarity search - Function
: / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Chem-AR6 / NICOTINAMIDE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / Retron Ec86 putative ribosyltransferase/DNA-binding protein / Retron Ec86 reverse transcriptase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang, Y.J. / Guan, Z.Y. / Wang, C. / Zou, T.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Rep / Year: 2024
Title: DNA methylation activates retron Ec86 filaments for antiphage defense.
Authors: Yanjing Wang / Chen Wang / Zeyuan Guan / Jie Cao / Jia Xu / Shuangshuang Wang / Yongqing Cui / Qiang Wang / Yibei Chen / Yongqi Yin / Delin Zhang / Hongbo Liu / Ming Sun / Shuangxia Jin / ...Authors: Yanjing Wang / Chen Wang / Zeyuan Guan / Jie Cao / Jia Xu / Shuangshuang Wang / Yongqing Cui / Qiang Wang / Yibei Chen / Yongqi Yin / Delin Zhang / Hongbo Liu / Ming Sun / Shuangxia Jin / Pan Tao / Tingting Zou /
Abstract: Retrons are a class of multigene antiphage defense systems typically consisting of a retron reverse transcriptase, a non-coding RNA, and a cognate effector. Although triggers for several retron ...Retrons are a class of multigene antiphage defense systems typically consisting of a retron reverse transcriptase, a non-coding RNA, and a cognate effector. Although triggers for several retron systems have been discovered recently, the complete mechanism by which these systems detect invading phages and mediate defense remains unclear. Here, we focus on the retron Ec86 defense system, elucidating its modes of activation and mechanisms of action. We identified a phage-encoded DNA cytosine methyltransferase (Dcm) as a trigger of the Ec86 system and demonstrated that Ec86 is activated upon multicopy single-stranded DNA (msDNA) methylation. We further elucidated the structure of a tripartite retron Ec86-effector filament assembly that is primed for activation by Dcm and capable of hydrolyzing nicotinamide adenine dinucleotide (NAD). These findings provide insights into the retron Ec86 defense mechanism and underscore an emerging theme of antiphage defense through supramolecular complex assemblies.
History
DepositionSep 20, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 18, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / em_admin ...chem_comp / em_admin / em_software / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _em_software.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.1Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Data processing / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata / EM metadata / Category: em_admin / em_software / entity
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Item: _chem_comp.name / _em_admin.last_update ..._chem_comp.name / _em_admin.last_update / _em_software.name / _entity.pdbx_description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retron Ec86 reverse transcriptase
C: Retron Ec86 putative ribosyltransferase/DNA-binding protein
D: DNA (85-MER)
E: RNA (82-MER)
F: RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')
B: Retron Ec86 reverse transcriptase
G: DNA (85-MER)
H: RNA (82-MER)
I: RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')
J: Retron Ec86 putative ribosyltransferase/DNA-binding protein
K: Retron Ec86 reverse transcriptase
L: Retron Ec86 putative ribosyltransferase/DNA-binding protein
M: DNA (85-MER)
N: RNA (82-MER)
O: RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')
P: Retron Ec86 reverse transcriptase
Q: DNA (85-MER)
R: RNA (82-MER)
S: RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')
T: Retron Ec86 putative ribosyltransferase/DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,41122
Polymers521,72920
Non-polymers6812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 2 types, 8 molecules ABKPCJLT

#1: Protein
Retron Ec86 reverse transcriptase / Ec86-RT / ORF320 / Reverse transcriptase / RT


Mass: 37832.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ret, LM2_00877 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23070, RNA-directed DNA polymerase
#2: Protein
Retron Ec86 putative ribosyltransferase/DNA-binding protein / ORF223


Mass: 35538.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LM2_00875 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DV88

-
DNA chain , 1 types, 4 molecules DGMQ

#3: DNA chain
DNA (85-MER)


Mass: 26320.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 341167

-
RNA chain , 2 types, 8 molecules EHNRFIOS

#4: RNA chain
RNA (82-MER)


Mass: 26199.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: msrRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 341167
#5: RNA chain
RNA (5'-R(P*CP*GP*UP*AP*AP*GP*GP*GP*UP*GP*CP*GP*CP*A)-3')


Mass: 4541.771 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 2 types, 2 molecules

#6: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: retron Ec86-effector fiber / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 270375 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429609
ELECTRON MICROSCOPYf_angle_d0.62942241
ELECTRON MICROSCOPYf_dihedral_angle_d27.1729100
ELECTRON MICROSCOPYf_chiral_restr0.0394965
ELECTRON MICROSCOPYf_plane_restr0.0043477

+
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