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- PDB-9g44: Structure of the minimal type I-F2 CRISPR-Cas DNA-interference co... -

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Basic information

Entry
Database: PDB / ID: 9g44
TitleStructure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.
Components
  • (CRISPR-associated ...) x 2
  • Cas5fv helical domain-containing protein
  • DEAD-like helicases-like protein
  • DNA (39-MER)
  • DNA (41-MER)
  • RNA (61-MER)
KeywordsANTIVIRAL PROTEIN / Type I-F2 CRISPR system / Nuclease-Helicase Cas3 / Structural characterization / Protein-DNA-RNA complex / Cryo-EM.
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / helicase activity / endonuclease activity / defense response to virus / nucleic acid binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
Cas5fv helical domain / : / : / Cas5fv helical domain / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily ...Cas5fv helical domain / : / : / Cas5fv helical domain / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / Cas3, HD domain / : / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / RNA / RNA (> 10) / DEAD-like helicases-like protein / Uncharacterized protein / Cas5fv helical domain-containing protein / CRISPR-associated protein, Csy4 family
Similarity search - Component
Biological speciesShewanella putrefaciens CN-32 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMais, C.N. / Perry, T.N. / Sanchez-Londono, M. / Steinchen, W. / Innis, C.A. / Randau, L. / Paush, P. / Bange, G.
Funding supportEuropean Union, Germany, 2items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)3869European Union
German Research Foundation (DFG)405858511 Germany
CitationJournal: To Be Published
Title: Structure of the minimal type I-F2 CRISPR-Cas DNA-interference complex.
Authors: Mais, C.N. / Perry, T.N. / Sanchez-Londono, M. / Steinchen, W. / Randau, L. / Innis, C.A. / Pausch, P. / Bange, G.
History
DepositionJul 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 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
C: CRISPR-associated protein, Csy4 family
F: CRISPR-associated protein Cas7
G: CRISPR-associated protein Cas7
H: CRISPR-associated protein Cas7
I: CRISPR-associated protein Cas7
J: RNA (61-MER)
K: DNA (39-MER)
L: DNA (41-MER)
B: Cas5fv helical domain-containing protein
A: DEAD-like helicases-like protein
D: CRISPR-associated protein Cas7
E: CRISPR-associated protein Cas7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)430,34914
Polymers430,30012
Non-polymers492
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-associated ... , 2 types, 7 molecules CFGHIDE

#1: Protein CRISPR-associated protein, Csy4 family


Mass: 19055.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1823 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Y6G3
#2: Protein
CRISPR-associated protein Cas7


Mass: 36481.035 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1821 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Y6G1

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DNA chain , 2 types, 2 molecules KL

#4: DNA chain DNA (39-MER)


Mass: 17248.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli (E. coli) / References: GenBank: 2321890520
#5: DNA chain DNA (41-MER)


Mass: 17946.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli (E. coli) / References: GenBank: 1780508237

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Protein , 2 types, 2 molecules BA

#6: Protein Cas5fv helical domain-containing protein


Mass: 37904.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1822 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Y6G2
#7: Protein DEAD-like helicases-like protein


Mass: 99727.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1820 / Production host: Escherichia coli (E. coli) / References: UniProt: A4Y6G0

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RNA chain / Non-polymers , 2 types, 3 molecules J

#3: RNA chain RNA (61-MER)


Mass: 19531.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli (E. coli) / References: GenBank: 1780508237
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: Type I-F2 Cascade-Cas3 effector complex. / Type: COMPLEX / Entity ID: #7, #6, #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Shewanella putrefaciens CN-32 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES sodium saltC8H17N2NaO4S1
2200 mMSodium chlorideNaCl1
320 mMPotassium chlorideKCl1
420 mMMagnesium chlorideMgCl21
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 defocus max: 1600 nm / Nominal defocus min: 400 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.7 sec. / Electron dose: 49.773 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7698
Image scansMovie frames/image: 37

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Processing

EM software
IDNameVersionCategory
1RELION5particle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
8PHENIXmodel refinement
10RELION5initial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2463680
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 250975 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00428989
ELECTRON MICROSCOPYf_angle_d0.49339773
ELECTRON MICROSCOPYf_dihedral_angle_d15.6274917
ELECTRON MICROSCOPYf_chiral_restr0.044465
ELECTRON MICROSCOPYf_plane_restr0.0034661

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