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- PDB-9jpf: crRNA-guided surveillance (Csy) complex -

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Basic information

Entry
Database: PDB / ID: 9jpf
TitlecrRNA-guided surveillance (Csy) complex
Components
  • RNA (49-MER)
  • Type I-F CRISPR-associated protein Csy1
  • Type I-F CRISPR-associated protein Csy2
  • Type I-F CRISPR-associated protein Csy3
KeywordsRNA BINDING PROTEIN/RNA / complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
RNA / RNA (> 10) / Type I-F CRISPR-associated protein Csy1 / Type I-F CRISPR-associated protein Csy2 / Type I-F CRISPR-associated protein Csy3
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWang, W.H. / Guan, L.L. / Du, X.Y. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000901 China
CitationJournal: To Be Published
Title: crRNA-guided surveillance (Csy) complex
Authors: Wang, W.H. / Guan, L.L. / Du, X.Y. / Feng, Y.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 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

Downloads & links

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Assembly

Deposited unit
A: Type I-F CRISPR-associated protein Csy1
B: Type I-F CRISPR-associated protein Csy2
C: Type I-F CRISPR-associated protein Csy3
D: Type I-F CRISPR-associated protein Csy3
E: Type I-F CRISPR-associated protein Csy3
F: Type I-F CRISPR-associated protein Csy3
G: RNA (49-MER)


Theoretical massNumber of molelcules
Total (without water)255,6087
Polymers255,6087
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

#1: Protein Type I-F CRISPR-associated protein Csy1


Mass: 53641.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: csy1, F7O97_17165
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A643IV20
#2: Protein Type I-F CRISPR-associated protein Csy2


Mass: 36093.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: csy2, F7O97_17160
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A643IWA1
#3: Protein
Type I-F CRISPR-associated protein Csy3


Mass: 37534.148 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: csy3, F7O97_17155
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A643IYA9
#4: RNA chain RNA (49-MER)


Mass: 15736.397 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
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: Cys complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: OTHER

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146897 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315262
ELECTRON MICROSCOPYf_angle_d0.55820849
ELECTRON MICROSCOPYf_dihedral_angle_d11.0442391
ELECTRON MICROSCOPYf_chiral_restr0.0422331
ELECTRON MICROSCOPYf_plane_restr0.0032665

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