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- PDB-8k23: ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composi... -

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Basic information

Entry
Database: PDB / ID: 8k23
TitleICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry
Components
  • Cas1
  • Csy1
  • Csy2
  • Csy3
  • Csy4
  • DNA (31-MER)
  • DNA (43-MER)
  • 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')
  • HD Cas3-type domain-containing protein
  • RNA (60-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 / DNA endonuclease activity / helicase activity / endonuclease 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 endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated endonuclease Cas1, N-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 endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / CRISPR-associated endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / Csy4 / Csy3 / Csy2 / Csy1 / 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: 3.75 Å
AuthorsZhang, L.X. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry
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: Additional map / Data content type: Additional map / 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 / _pdbx_entry_details.has_protein_modification
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
B: Csy1
C: Csy2
D: Cas1
E: Cas1
G: Csy3
H: Csy4
I: Csy3
J: Csy3
K: Csy3
L: Csy3
M: Csy3
P: RNA (60-MER)
Q: DNA (43-MER)
R: DNA (31-MER)
A: HD Cas3-type domain-containing protein
U: DNA (43-MER)
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
b: Csy1
c: Csy2
d: Cas1
e: Cas1
g: Csy3
h: Csy4
i: Csy3
j: Csy3
k: Csy3
l: Csy3
m: Csy3
p: RNA (60-MER)
q: DNA (43-MER)
r: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)983,70836
Polymers983,48832
Non-polymers2204
Water00
1


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

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Components

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Protein , 6 types, 24 molecules BbCcDEdeGIJKLMgijklmHhAa

#1: Protein Csy1


Mass: 20224.736 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_00450 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V8
#2: Protein Csy2


Mass: 27401.547 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_00445 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V7
#3: Protein
Cas1


Mass: 34286.137 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
#4: Protein
Csy3


Mass: 33399.301 Da / Num. of mol.: 12
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
#5: Protein Csy4


Mass: 18736.680 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_00435 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V5
#9: Protein HD Cas3-type domain-containing protein


Mass: 104703.031 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

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DNA chain , 3 types, 6 molecules QUqRrV

#7: DNA chain DNA (43-MER)


Mass: 13431.698 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)
#8: DNA chain DNA (31-MER)


Mass: 9346.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)
#10: 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)

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RNA chain / Non-polymers , 2 types, 6 molecules Pp

#11: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: RNA chain RNA (60-MER)


Mass: 19046.227 Da / Num. of mol.: 2
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 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: csy complex / Type: COMPLEX / Entity ID: #1-#10 / 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: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 132865 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00640544
ELECTRON MICROSCOPYf_angle_d1.13355680
ELECTRON MICROSCOPYf_dihedral_angle_d18.5126786
ELECTRON MICROSCOPYf_chiral_restr0.066337
ELECTRON MICROSCOPYf_plane_restr0.0086530

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