[English] 日本語
Yorodumi
- EMDB-73096: Cryo-EM structure of the CbCash filament bound to cA4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-73096
TitleCryo-EM structure of the CbCash filament bound to cA4
Map dataCbCash Filament
Sample
  • Complex: Octonary complex of CbCash filament with Cyclic tetraadenylate
    • Protein or peptide: CbCash
    • RNA: Cyclic tetraadenylate
KeywordstRNA endonuclease / cA4 activation / CRISPR associated Schlafen / Csx15 / RNA BINDING PROTEIN
Biological speciesChloroflexia (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.45 Å
AuthorsLiu Y / Weickert P / Strecker J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Prokaryotic Schlafen proteins cleave tRNAs during type III CRISPR immunity.
Authors: Pedro Weickert / Yang Liu / Jonathan Strecker /
Abstract: Schlafen nucleases restrict viral infection in mammals by cleaving self RNAs, however, their function and mechanism in prokaryotic immunity is unknown. Here, we uncover CRISPR-associated Schlafen ...Schlafen nucleases restrict viral infection in mammals by cleaving self RNAs, however, their function and mechanism in prokaryotic immunity is unknown. Here, we uncover CRISPR-associated Schlafen (Cash) proteins containing a Schlafen domain fused to Csx15, an uncharacterized member of Rossmann-like nucleotide-binding sensors. Cash is activated by cyclic tetra-adenylate (cA₄) produced during type III CRISPR interference and induces cell toxicity by cleaving tRNAs, primarily in the T-loop. Cryo-electron microscopy structures of Chloroflexi bacterium Cash reveal an inactive dodecamer, the formation of a filament upon cA₄ binding to align catalytic interfaces, and the molecular basis of substrate recognition and cleavage in a tRNA-bound complex. We identify numerous families of prokaryotic Schlafen proteins associated with diverse antiviral defense systems and characterized by unique sensor domains. This work highlights tRNA depletion by Schlafen nucleases as an evolutionary recurring antiviral strategy and reveals mechanistic differences between Cash and human Schlafen members.
History
DepositionOct 9, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_73096.png

Downloads & links

-
Map

FileDownload / File: emd_73096.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCbCash Filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 416 pix.
= 351.104 Å		0.84 Å/pix.
x 416 pix.
= 351.104 Å		0.84 Å/pix.
x 416 pix.
= 351.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.115
Minimum - Maximum-1.3373878 - 2.302552
Average (Standard dev.)0.00034471863 (±0.037163496)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 351.104 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_73096_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_73096_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_73096_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Octonary complex of CbCash filament with Cyclic tetraadenylate

EntireName: Octonary complex of CbCash filament with Cyclic tetraadenylate
Components
  • Complex: Octonary complex of CbCash filament with Cyclic tetraadenylate
    • Protein or peptide: CbCash
    • RNA: Cyclic tetraadenylate

-
Supramolecule #1: Octonary complex of CbCash filament with Cyclic tetraadenylate

SupramoleculeName: Octonary complex of CbCash filament with Cyclic tetraadenylate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chloroflexia (bacteria)
Molecular weightTheoretical: 273.19 kDa/nm

-
Macromolecule #1: CbCash

MacromoleculeName: CbCash / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chloroflexia (bacteria)
Molecular weightTheoretical: 33.530633 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDKLWRLLGN YVDSGRETRK VDLKREIEMK AGAGKFAKDV AAIANTIGGT GYLIIGVIDL KERKSNSPDD YVTGWNVTDL DGFSRWVNQ SLSNYCNPIP RIEIEEMTHP VCGKKIGVII IPRSLDCPHE IIRDGDGITK GMYVRRGADT FTASREELRA M MGGTDVRI ...String:
MDKLWRLLGN YVDSGRETRK VDLKREIEMK AGAGKFAKDV AAIANTIGGT GYLIIGVIDL KERKSNSPDD YVTGWNVTDL DGFSRWVNQ SLSNYCNPIP RIEIEEMTHP VCGKKIGVII IPRSLDCPHE IIRDGDGITK GMYVRRGADT FTASREELRA M MGGTDVRI VLNFLQPLTQ LNREQIGQYL NARVYEVLEP RSLPIRLDEN LSFVEQAKIL LNETGLTPEE WRTLPLIVNL PG FSPLSSI LLAEMQGRMS RLPHIIRMRP TPADRTIFEV AEVIALQDIR DKALEWSSGI

-
Macromolecule #2: Cyclic tetraadenylate

MacromoleculeName: Cyclic tetraadenylate / type: rna / ID: 2 / Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.271866 KDa
SequenceString:
AAAA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
200.0 mMNaClsodium chloride
5.0 mMMgCl2magnicium chloride
1.0 mMTCEPtris(2-carboxyethyl)phosphine

Details: 25mM HEPES pH 7.5, 200mM NaCl, 5mM MgCl2, 1mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot Force 15 Wait Time 0s Blot Time 3.5s.
DetailsCbCash proteins incubated with cA4 at 100uM.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.1) / Number images used: 1008367
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: cryoSPARC ab initio
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9ylx:
Cryo-EM structure of the CbCash filament bound to cA4

+
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