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- PDB-7jzy: CryoEM structure of a CRISPR-Cas complex -

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Basic information

Entry
Database: PDB / ID: 7jzy
TitleCryoEM structure of a CRISPR-Cas complex
Components
  • (Type I-F CRISPR-associated ...) x 2
  • AcrF9
  • CRISPR type I-F/YPEST-associated protein Csy3
  • CRISPR-associated protein Csy1
  • RNA (61-MER)
KeywordsHYDROLASE/RNA / CRISPR / HYDROLASE-RNA complex
Function / homology
Function and homology information


defense response to virus
Similarity search - Function
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) / CRISPR type I-F/YPEST-associated protein Csy3 / : / Uncharacterized protein / CRISPR-associated protein Csy1
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChang, L. / Li, Z. / Gabel, C.
CitationJournal: To Be Published
Title: CryoEM structure of a CRISPR-Cas complex
Authors: Chang, L. / Li, Z. / Gabel, C.
History
DepositionSep 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.0Sep 22, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 22, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 22, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Sep 22, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 22, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Jun 4, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-22584
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein Csy1
B: Type I-F CRISPR-associated protein Csy2
C: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4
M: RNA (61-MER)
D: CRISPR type I-F/YPEST-associated protein Csy3
E: CRISPR type I-F/YPEST-associated protein Csy3
F: CRISPR type I-F/YPEST-associated protein Csy3
G: CRISPR type I-F/YPEST-associated protein Csy3
H: CRISPR type I-F/YPEST-associated protein Csy3
I: CRISPR type I-F/YPEST-associated protein Csy3
J: AcrF9
K: AcrF9


Theoretical massNumber of molelcules
Total (without water)367,75612
Polymers367,75612
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area60220 Å2
ΔGint-187 kcal/mol
Surface area120570 Å2

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Components

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Protein , 3 types, 9 molecules ADEFGHIJK

#1: Protein CRISPR-associated protein Csy1 / Csy1 (Cas8f)


Mass: 49194.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: csy1, PA14_33330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02ML9
#5: Protein
CRISPR type I-F/YPEST-associated protein Csy3 / CRISPR-associated protein Csy3


Mass: 37579.273 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: EQH76_13805, F7O93_18150, NCTC13437_01527, NCTC13619_03982
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A444M080
#6: Protein AcrF9


Mass: 7813.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Type I-F CRISPR-associated ... , 2 types, 2 molecules BC

#2: Protein Type I-F CRISPR-associated protein Csy2 / Csy2 (Cas5f)


Mass: 36244.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: csy2, ALP65_00953, EQH76_13810, FCG96_17775, PACL_0128
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B3G161
#3: Protein Type I-F CRISPR-associated endoribonuclease Cas6/Csy4


Mass: 21675.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cas6f, F7O93_18155 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A643HZS6

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RNA chain , 1 types, 1 molecules M

#4: RNA chain RNA (61-MER)


Mass: 19538.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: GenBank: 313291946

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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: CRISPR-Cas complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150697 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00925143
ELECTRON MICROSCOPYf_angle_d0.96734415
ELECTRON MICROSCOPYf_dihedral_angle_d21.6229357
ELECTRON MICROSCOPYf_chiral_restr0.0533885
ELECTRON MICROSCOPYf_plane_restr0.0064315

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