[English] 日本語
Yorodumi
- PDB-9svk: cryo-EM structure of LwHicAB-crRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9svk
Titlecryo-EM structure of LwHicAB-crRNA
Components
  • RNA (58-MER)
  • Toxin-antitoxin system, antitoxin component, HicB family
  • Toxin-antitoxin system, toxin component, HicA family
KeywordsIMMUNE SYSTEM / toxin-antitoxin / CRISPR RNA binding / prokaryotic immunity
Function / homologyHicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / TTHA1013/TTHA0281-like / mRNA binding / RNA / RNA (> 10) / Toxin-antitoxin system, toxin component, HicA family / Toxin-antitoxin system, antitoxin component, HicB family
Function and homology information
Biological speciesLeptotrichia wadei F0279 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiang, L. / Jiyun, C. / Xueyan, L.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105184332 United Kingdom
Wellcome TrustWT096570 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 937-2022European Union
CitationJournal: Nat Commun / Year: 2026
Title: Potential role of a CRISPR-Cas-activated toxin-antitoxin system in bacterial immunity.
Authors: Jiyun Chen / Linglong Huang / Hong Chen / Xueyan Li / Xiaofeng Lin / Chenmin Guo / Xi Liu / Guowei Fu / Ying Chen / Liang Liu /
Abstract: CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. In typical toxin-antitoxin systems, toxin activation can limit phage propagation by inducing growth ...CRISPR-Cas and toxin-antitoxin systems can serve as antiviral defense mechanisms in prokaryotes. In typical toxin-antitoxin systems, toxin activation can limit phage propagation by inducing growth arrest or reduced cellular fitness, while the antitoxin neutralizes toxin activity. Here, we study potential functional synergy between a CRISPR-Cas13a system and a type II toxin-antitoxin module (HicAB) from a Leptotrichia bacterium, when heterologously expressed in E. coli, as well as in biochemical and structural analyses. We show that the antitoxin HicB exhibits toxic properties, and Cas13a directly activates HicB, triggering growth inhibition and conferring protection against bacteriophages. Structural analyses reveal that Cas13a binding promotes the spatial proximity of HicB tetramers, likely enabling its activation. The toxin HicA competitively binds to HicB, thereby inhibiting Cas13a-mediated HicB activation. Importantly, both CRISPR RNA and HicB independently suppress HicA toxicity. Structural evidence indicates that CRISPR RNA forms a hetero-tetradecameric complex with HicAB, occluding HicA's active site and neutralizing its toxic function. Thus, our findings indicate functional synergy between distinct bacterial immune strategies.
History
DepositionOct 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Toxin-antitoxin system, antitoxin component, HicB family
C: Toxin-antitoxin system, antitoxin component, HicB family
A: Toxin-antitoxin system, toxin component, HicA family
D: Toxin-antitoxin system, antitoxin component, HicB family
E: Toxin-antitoxin system, antitoxin component, HicB family
F: Toxin-antitoxin system, toxin component, HicA family
G: Toxin-antitoxin system, antitoxin component, HicB family
H: Toxin-antitoxin system, antitoxin component, HicB family
I: Toxin-antitoxin system, toxin component, HicA family
J: Toxin-antitoxin system, antitoxin component, HicB family
K: Toxin-antitoxin system, antitoxin component, HicB family
L: Toxin-antitoxin system, toxin component, HicA family
M: RNA (58-MER)
N: RNA (58-MER)


Theoretical massNumber of molelcules
Total (without water)193,02414
Polymers193,02414
Non-polymers00
Water00
1


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

-
Components

#1: Protein
Toxin-antitoxin system, antitoxin component, HicB family


Mass: 15867.150 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia wadei F0279 (bacteria) / Gene: HMPREF9015_01859 / Production host: Escherichia coli (E. coli) / References: UniProt: U2RCH0
#2: Protein
Toxin-antitoxin system, toxin component, HicA family


Mass: 7239.685 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia wadei F0279 (bacteria) / Gene: HMPREF9015_01860 / Production host: Escherichia coli (E. coli) / References: UniProt: U2R460
#3: RNA chain RNA (58-MER)


Mass: 18564.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia wadei F0279 (bacteria) / Production host: Escherichia phage T7 (virus)
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: LwHicAB-crRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Leptotrichia wadei F0279 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2100 mMsodium chlorideNaCl1
31 mMDTTC4H10O2S21
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 63 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
7Cootmodel fitting
12RELION3D reconstruction
13PHENIX1.17.1_3660:model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1184599 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00512333
ELECTRON MICROSCOPYf_angle_d0.65916883
ELECTRON MICROSCOPYf_dihedral_angle_d19.4454774
ELECTRON MICROSCOPYf_chiral_restr0.0421939
ELECTRON MICROSCOPYf_plane_restr0.0041940

+
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