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- PDB-8k28: ICP1 Csy-dsDNA complex (form 1) -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8k28
TitleICP1 Csy-dsDNA complex (form 1)
Components
  • Csy1
  • Csy2
  • Csy3
  • Csy4
  • DNA (27-MER)
  • DNA (33-MER)
  • RNA (59-MER)
KeywordsRNA BINDING PROTEIN/DNA/RNA / IMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity
Similarity search - Function
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) / Csy4 / Csy3 / Csy2 / Csy1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZhang, L.X. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: Structure of csy complex with long DNA State1
Authors: Zhang, L.X. / Feng, Y.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 17, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 23, 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csy1
B: Csy2
C: Csy3
D: Csy3
E: Csy3
F: Csy3
G: Csy3
I: Csy4
Q: DNA (33-MER)
R: DNA (27-MER)
P: RNA (59-MER)
H: Csy3


Theoretical massNumber of molelcules
Total (without water)304,13012
Polymers304,13012
Non-polymers00
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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Protein , 4 types, 9 molecules ABCDEFGHI

#1: Protein Csy1


Mass: 20409.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00450 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V8
#2: Protein Csy2


Mass: 27401.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V7
#3: Protein
Csy3


Mass: 33399.301 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00440 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V6
#4: Protein Csy4


Mass: 18736.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00435 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V5

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DNA chain , 2 types, 2 molecules QR

#5: DNA chain DNA (33-MER)


Mass: 10154.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (27-MER)


Mass: 8330.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)

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RNA chain , 1 types, 1 molecules P

#7: RNA chain RNA (59-MER)


Mass: 18701.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)

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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: csy complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90717 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01421388
ELECTRON MICROSCOPYf_angle_d0.80529526
ELECTRON MICROSCOPYf_dihedral_angle_d18.7073841
ELECTRON MICROSCOPYf_chiral_restr0.0453430
ELECTRON MICROSCOPYf_plane_restr0.0063398

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