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- PDB-9zs2: S. marcescens Cas10-Csm unbound to target RNA -

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Basic information

Entry
Database: PDB / ID: 9zs2
TitleS. marcescens Cas10-Csm unbound to target RNA
Components
  • CRISPR system Cms endoribonuclease Csm3
  • CRISPR system Cms protein Csm4
  • CRISPR system Cms protein Csm5
  • CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
  • RNA (30-MER)
KeywordsRNA BINDING PROTEIN / CRISPR / crRNA / Cas10 / type III
Function / homology
Function and homology information


exonuclease activity / transferase activity / endonuclease activity / defense response to virus / hydrolase activity / RNA binding / ATP binding
Similarity search - Function
CRISPR-associated protein Csm5 / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / : ...CRISPR-associated protein Csm5 / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / : / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR system Cms protein Csm5 / CRISPR system Cms endoribonuclease Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system Cms protein Csm4
Similarity search - Component
Biological speciesSerratia (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPerdigao, C.C. / Dokland, T. / Dunkle, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142966 United States
National Institutes of Health/Office of the DirectorS10OD024978 United States
CitationJournal: bioRxiv / Year: 2026
Title: Structural insights into target detection by the type III CRISPR complex and its deployment in SNP identification.
Authors: Calvin C Perdigao / Luqman O Ajisafe / Anju T Sunny / Si Wu / Terje Dokland / Jack A Dunkle /
Abstract: Type III CRISPR systems utilize a complex containing Cas10, additional Cas proteins and a crRNA to detect foreign transcripts. Upon detection, Cas10 synthesizes cyclic oligoadenylates (cOA), ...Type III CRISPR systems utilize a complex containing Cas10, additional Cas proteins and a crRNA to detect foreign transcripts. Upon detection, Cas10 synthesizes cyclic oligoadenylates (cOA), signaling molecules that coordinate interference by stimulating downstream enzymes with DNase, RNase, protease or other activities. Type III systems are among the most abundant CRISPR systems in prokaryotes and understanding the structure-function relationships that control transcript detection and cOA synthesis will advance the understanding of the broader physiological roles of these systems. Type III systems possess properties well-suited to their deployment as molecule diagnostics: specific detection and activation of a cascade of multi-turnover enzymatic reactions that can be harnessed for signal generation. We determined that Cas10-Csm (SmCas10-Csm) synthesizes predominantly cA molecules and this synthesis is sensitive to mismatches in the crRNA-target RNA duplex adjacent to Cas10. We determined the structure of SmCas10-Csm unbound and bound to target RNA identifying conformational changes associated with target binding. We demonstrate that SmCas10-Csm can distinguish between single nucleotide polymorphisms that occur in the human transcript that are associated with sickle cell disease indicating an additional role for type III CRISPR systems in point-of-care diagnostics in low-resource settings.
History
DepositionDec 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
E: CRISPR system Cms endoribonuclease Csm3
F: CRISPR system Cms endoribonuclease Csm3
G: CRISPR system Cms endoribonuclease Csm3
H: CRISPR system Cms endoribonuclease Csm3
I: CRISPR system Cms protein Csm4
J: CRISPR system Cms protein Csm5
K: RNA (30-MER)


Theoretical massNumber of molelcules
Total (without water)311,4158
Polymers311,4158
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / Cyclic oligoadenylate synthase


Mass: 90390.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: cas10, CWC46_19900, Ser39006_019895 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TNR6
#2: Protein
CRISPR system Cms endoribonuclease Csm3 / CRISPR type III A-associated RAMP protein Csm3


Mass: 27185.859 Da / Num. of mol.: 4 / Mutation: D43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: csm3, CWC46_19910, Ser39006_019905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TNQ0
#3: Protein CRISPR system Cms protein Csm4


Mass: 35770.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: CWC46_19915, Ser39006_019910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TQV2
#4: Protein CRISPR system Cms protein Csm5 / CRISPR type III A-associated protein Csm5


Mass: 63148.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: CWC46_19920, Ser39006_019915 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TBB3
#5: RNA chain RNA (30-MER)


Mass: 13361.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Cas10-Csm / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Serratia (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARC4CTF correction
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42471 / Symmetry type: POINT
RefinementCross valid method: NONE

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