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- PDB-8k21: Cas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex -

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Basic information

Entry
Database: PDB / ID: 8k21
TitleCas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex
Components
  • Cas1
  • DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')
  • HD Cas3-type domain-containing protein
KeywordsANTIBIOTIC/RNA BINDING PROTEIN/DNA / IMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC-RNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / helicase activity / defense response to virus / hydrolase activity / DNA binding / ATP binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, YPEST subtype / : / 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 endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain ...CRISPR-associated protein Cas1, YPEST subtype / : / 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 endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / HD Cas3-type domain-containing protein / Cas1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 short DNA
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 16, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 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
U: DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')
V: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')
A: HD Cas3-type domain-containing protein
D: Cas1
E: Cas1
a: HD Cas3-type domain-containing protein
d: Cas1
e: Cas1


Theoretical massNumber of molelcules
Total (without water)163,5048
Polymers163,5048
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

#1: DNA chain DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')


Mass: 6543.286 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)
#2: DNA chain DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')


Mass: 6338.120 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)
#3: Protein HD Cas3-type domain-containing protein


Mass: 8332.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00455 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V9
#4: Protein
Cas1


Mass: 33489.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00460 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5W0
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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30241 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811754
ELECTRON MICROSCOPYf_angle_d1.26216051
ELECTRON MICROSCOPYf_dihedral_angle_d18.4041861
ELECTRON MICROSCOPYf_chiral_restr0.0711783
ELECTRON MICROSCOPYf_plane_restr0.0081884

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