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- PDB-9zs4: S. marcescens Cas10-Csm bound to target RNA -

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Basic information

Entry
Database: PDB / ID: 9zs4
TitleS. marcescens Cas10-Csm bound to target RNA
Components
  • (CRISPR system ...) x 5
  • Target RNA
  • crRNA
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, Csm2 Type III-A / CRISPR-associated protein Csm5 / Csm2 Type III-A / 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 / : / : ...CRISPR-associated protein, Csm2 Type III-A / CRISPR-associated protein Csm5 / Csm2 Type III-A / 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 protein Csm2 / 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: 3.8 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: To Be Published
Title: Structural insights into target detection by the S. marcescens type III CRISPR complex and its deployment in SNP identification
Authors: Perdigao, C.C. / Ajisafe, L.O. / Sunny, A.T. / Wu, S. / Dokland, T. / Dunkle, J.A.
History
DepositionDec 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 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)
K: crRNA
L: Target RNA
B: CRISPR system Cms protein Csm2
C: CRISPR system Cms protein Csm2
D: CRISPR system Cms protein Csm2
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


Theoretical massNumber of molelcules
Total (without water)372,63412
Polymers372,63412
Non-polymers00
Water00
1


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

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Components

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CRISPR system ... , 5 types, 10 molecules ABCDEFGHIJ

#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
#4: Protein CRISPR system Cms protein Csm2 / CRISPR type III A-associated protein Csm2


Mass: 15886.099 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia (bacteria) / Gene: csm2, CWC46_19905, Ser39006_019900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2I5TBC8
#5: Protein
CRISPR system Cms endoribonuclease Csm3 / CRISPR type III A-associated RAMP protein Csm3


Mass: 27185.859 Da / Num. of mol.: 4 / Mutation: D34A
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
#6: 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
#7: 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

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RNA chain , 2 types, 2 molecules KL

#2: RNA chain crRNA


Mass: 13361.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Serratia (bacteria)
#3: RNA chain Target RNA


Mass: 13560.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Serratia (bacteria)

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Details

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 bound to target RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.34 MDa / Experimental value: NO
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: 3000 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
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129762 / Symmetry type: POINT
RefinementCross valid method: NONE

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