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- PDB-5gqh: Cryo-EM structure of PaeCas3-AcrF3 complex -

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Basic information

Entry
Database: PDB / ID: 5gqh
TitleCryo-EM structure of PaeCas3-AcrF3 complex
Components
  • CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
  • anti-CRISPR protein 3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CRISPR/Cas system anti-CRISPR proteins Cas3 AcrF3 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / CRISPR-associated nuclease/helicase Cas3, C-terminal / CRISPR-associated Cas3-type HD domain ...: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / Cas3, HD domain / CRISPR-associated nuclease/helicase Cas3, C-terminal / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / HD Cas3-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phage protein / CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
Pseudomonas phage JBD5 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang, X. / Ma, J. / Wang, Y. / Wang, J.
CitationJournal: Cell Res / Year: 2016
Title: A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses.
Authors: Jiuyu Wang / Jun Ma / Zhi Cheng / Xu Meng / Lilan You / Min Wang / Xinzheng Zhang / Yanli Wang /
History
DepositionAug 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / em_image_scans / Item: _cell.Z_PDB
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
B: anti-CRISPR protein 3
C: anti-CRISPR protein 3


Theoretical massNumber of molelcules
Total (without water)154,5053
Polymers154,5053
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST / type I-F CRISPR-associated nuclease/helicase Cas3


Mass: 122892.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Strain: UCBPP-PA14 / Gene: cas3 / Production host: Escherichia Coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q02ML8, Hydrolases; Acting on ester bonds, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein anti-CRISPR protein 3 / AcrF3 / Uncharacterized protein


Mass: 15806.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage JBD5 (virus) / Gene: JBD5_035 / Production host: Escherichia Coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: L7P7R7

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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

Component
IDNameTypeEntity IDParent-IDSource
1PaeCas3-AcrF3 complexCOMPLEXall0MULTIPLE SOURCES
2type I-F CRISPR-associated nuclease/helicase Cas3COMPLEX#11RECOMBINANT
3anti-CRISPR protein 3 (AcrF3)COMPLEX#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pseudomonas aeruginosa (bacteria)287
23Pseudomonas phage JBD5 (virus)1223261
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDPlasmid
12Escherichia Coli BL21(DE3) (bacteria)469008pET
23Escherichia Coli BL21(DE3) (bacteria)469008pET
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 78904 / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL

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