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- PDB-6whi: Cryo-electron microscopy structure of the type I-F CRISPR RNA-gui... -

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Basic information

Entry
Database: PDB / ID: 6whi
TitleCryo-electron microscopy structure of the type I-F CRISPR RNA-guided surveillance complex bound to the anti-CRISPR AcrIF9
Components
  • (CRISPR-associated protein ...) x 2
  • (non-target dsDNA) x 2
  • CRISPR-associated endonuclease Cas6/Csy4
  • RNA (60-MER)
  • Type I-F CRISPR-associated protein Csy2
  • anti-CRISPR AcrIF9
KeywordsIMMUNE SYSTEM/DNA/RNA / type I-F CRISPR RNA-guided surveillance complex / Csy complex / IMMUNE SYSTEM-DNA-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
CRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3)
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR type I-F/YPEST-associated protein Csy3 / Uncharacterized protein / SH3b domain-containing protein / CRISPR-associated protein Csy1 / CRISPR-associated protein Csy2 ...: / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR type I-F/YPEST-associated protein Csy3 / Uncharacterized protein / SH3b domain-containing protein / CRISPR-associated protein Csy1 / CRISPR-associated protein Csy2 / CRISPR-associated protein Csy3 / CRISPR-associated endonuclease Cas6/Csy4
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Proteus penneri (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsHirschi, M. / Santiago-Frangos, A. / Wilkinson, R. / Golden, S.M. / Wiedenheft, B. / Lander, G.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorDP2EB020402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867 United States
National Institutes of Health/Office of the DirectorS10OD021634 United States
CitationJournal: Nat Commun / Year: 2020
Title: AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex.
Authors: Marscha Hirschi / Wang-Ting Lu / Andrew Santiago-Frangos / Royce Wilkinson / Sarah M Golden / Alan R Davidson / Gabriel C Lander / Blake Wiedenheft /
Abstract: Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of ...Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 6, 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 protein Csy1
B: Type I-F CRISPR-associated protein Csy2
C: CRISPR-associated protein Csy3
D: CRISPR-associated protein Csy3
E: CRISPR-associated protein Csy3
F: CRISPR-associated protein Csy3
G: CRISPR-associated protein Csy3
H: CRISPR-associated protein Csy3
M: RNA (60-MER)
L: CRISPR-associated endonuclease Cas6/Csy4
I: anti-CRISPR AcrIF9
J: anti-CRISPR AcrIF9
N: non-target dsDNA
Q: non-target dsDNA
P: non-target dsDNA
O: non-target dsDNA


Theoretical massNumber of molelcules
Total (without water)475,49916
Polymers475,49916
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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CRISPR-associated protein ... , 2 types, 7 molecules ACDEFGH

#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 (E. coli) / References: UniProt: Q02ML9
#3: Protein
CRISPR-associated protein Csy3 / Csy3 (Cas7f)


Mass: 39778.594 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: EQH76_13805, FCG96_17770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A444M080, UniProt: Q02MM1*PLUS

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Protein , 3 types, 4 molecules BLIJ

#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 (E. coli) / References: UniProt: B3G161, UniProt: Q02MM0*PLUS
#5: Protein CRISPR-associated endonuclease Cas6/Csy4 / Csy4 (Cas6f)


Mass: 21427.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: cas6f, csy4, PA14_33300 / Production host: Escherichia coli (E. coli)
References: UniProt: Q02MM2, Hydrolases; Acting on ester bonds
#6: Protein anti-CRISPR AcrIF9


Mass: 7863.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus penneri (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: C0AVY5

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RNA chain , 1 types, 1 molecules M

#4: RNA chain RNA (60-MER)


Mass: 19265.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 313291946

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DNA chain , 2 types, 4 molecules NQPO

#7: DNA chain non-target dsDNA


Mass: 23797.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)
#8: DNA chain non-target dsDNA


Mass: 23687.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pseudomonas aeruginosa (bacteria)

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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
1Ternary complex of the type I-F CRISPR RNA-guided surveillance complex with the anti-CRISPR AcrIF9 and non-specific double stranded DNACOMPLEXall0MULTIPLE SOURCES
2type I-F crRNA-guided CRISPR surveillance complexCOMPLEX#1-#5, #7-#81RECOMBINANT
3Anti-CRISPR AcrIF9COMPLEX#61RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Pseudomonas aeruginosa (bacteria)287
23Proteus penneri (bacteria)102862
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenConc.: 1.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 11.5 sec. / Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6472
Image scansMovie frames/image: 120

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Processing

CTF correctionType: NONE
Particle selectionNum. of particles selected: 1049173
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152066 / Symmetry type: POINT

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