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- PDB-9n3z: Type IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - l... -

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Basic information

Entry
Database: PDB / ID: 9n3z
TitleType IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - locked state
Components
  • (CRISPR type AFERR-associated protein ...) x 3
  • CCRISPR type AFERR-associated protein Csf3 (Cas5)
  • CRISPR-associated DEAD/DEAH-box helicase CasDinG
  • DNA, non-target strand (47-MER)
  • DNA, target strand (47-MER)
  • crRNA (61-MER)
KeywordsDNA BINDING PROTEIN / CRISPR / transcriptional regulation / helicase
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleobase-containing compound metabolic process / helicase activity / nucleic acid binding / ATP binding / metal ion binding
Similarity search - Function
: / CRISPR-associated protein Csf1 / CRISPR type IV associated protein Csf3 / : / Type IV CRISPR-associated endonuclease Csf5 / CRISPR-associated protein, Csf1 family / CRISPR type IV/AFERR-associated protein Csf2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CasDinG / Csf1 / Csf3 / Csf2 / Csf5
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsKiernan, K.A. / Taylor, D.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138348 United States
Welch FoundationF-1938-20200401 United States
American Cancer SocietyRSG-21-050-01-DMC United States
CitationJournal: To Be Published
Title: Locked and loaded: mechanisms of CasDinG recruitment to the type IV-A1 CRISPR effector complex
Authors: Kiernan, K.A. / Taylor, D.W.
History
DepositionFeb 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 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: CRISPR type AFERR-associated protein Csf1 (Cas8)
B: CCRISPR type AFERR-associated protein Csf3 (Cas5)
C: CRISPR type AFERR-associated protein Csf2 (Cas7)
D: CRISPR type AFERR-associated protein Csf2 (Cas7)
E: CRISPR type AFERR-associated protein Csf2 (Cas7)
F: CRISPR type AFERR-associated protein Csf2 (Cas7)
G: CRISPR type AFERR-associated protein Csf2 (Cas7)
H: CRISPR type AFERR-associated protein Csf5 (Cas6)
I: crRNA (61-MER)
J: DNA, non-target strand (47-MER)
K: DNA, target strand (47-MER)
L: CRISPR-associated DEAD/DEAH-box helicase CasDinG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,94313
Polymers399,87712
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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CRISPR type AFERR-associated protein ... , 3 types, 7 molecules ACDEFGH

#1: Protein CRISPR type AFERR-associated protein Csf1 (Cas8) / Csf1


Mass: 27036.002 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: UniProt: A0AAB0B1U3
#3: Protein
CRISPR type AFERR-associated protein Csf2 (Cas7) / Csf2


Mass: 38623.707 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAB0B1V3
#4: Protein CRISPR type AFERR-associated protein Csf5 (Cas6) / Csf5


Mass: 25398.381 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: UniProt: A0AAB0B1V7

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Protein , 2 types, 2 molecules BL

#2: Protein CCRISPR type AFERR-associated protein Csf3 (Cas5) / Csf3


Mass: 24421.953 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: UniProt: A0AAB0B1V2
#8: Protein CRISPR-associated DEAD/DEAH-box helicase CasDinG / CasDinG


Mass: 81111.812 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: UniProt: A0AA82WPF0

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DNA chain , 2 types, 2 molecules JK

#6: DNA chain DNA, non-target strand (47-MER)


Mass: 14603.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA, target strand (47-MER)


Mass: 14349.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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RNA chain / Non-polymers , 2 types, 2 molecules I

#5: RNA chain crRNA (61-MER)


Mass: 19837.855 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)
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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 IV-A1 effector complex bound to CasDinG (locked state)
Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38045 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7XG3

7xg3


Accession code: 7XG3 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00526073
ELECTRON MICROSCOPYf_angle_d0.90636097
ELECTRON MICROSCOPYf_dihedral_angle_d22.4125108
ELECTRON MICROSCOPYf_chiral_restr0.0534123
ELECTRON MICROSCOPYf_plane_restr0.0084125

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