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- EMDB-36824: Cas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36824
TitleCas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex
Map data
Sample
  • Complex: csy complex
    • DNA: 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')
    • DNA: 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')
    • Protein or peptide: HD Cas3-type domain-containing protein
    • Protein or peptide: Cas1
KeywordsIMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC/RNA BINDING PROTEIN/DNA / 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
HD Cas3-type domain-containing protein / Cas1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang LX / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: Structure of csy complex with short DNA
Authors: Zhang LX / Feng Y
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36824.png

Downloads & links

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Map

FileDownload / File: emd_36824.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å		1.1 Å/pix.
x 240 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.020004718 - 0.05410519
Average (Standard dev.)0.00026595965 (±0.002293286)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36824_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36824_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : csy complex

EntireName: csy complex
Components
  • Complex: csy complex
    • DNA: 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')
    • DNA: 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')
    • Protein or peptide: HD Cas3-type domain-containing protein
    • Protein or peptide: Cas1

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Supramolecule #1: csy complex

SupramoleculeName: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)

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Macromolecule #1: DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP...

MacromoleculeName: 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')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 6.543286 KDa
SequenceString:
(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DT)(DA)(DA) (DA)(DT)(DA)(DG)(DG)(DG)(DA)(DA)(DG)(DA) (DT)

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Macromolecule #2: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*...

MacromoleculeName: 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')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 6.33812 KDa
SequenceString:
(DA)(DT)(DC)(DT)(DT)(DC)(DC)(DC)(DT)(DA) (DT)(DT)(DT)(DA)(DA)(DA)(DT)(DT)(DG)(DC) (DT)

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Macromolecule #3: HD Cas3-type domain-containing protein

MacromoleculeName: HD Cas3-type domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 8.332723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAM

UniProtKB: HD Cas3-type domain-containing protein

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Macromolecule #4: Cas1

MacromoleculeName: Cas1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 33.489379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH ...String:
MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH EGTFVKSLYK EYALEYEIEF KRDHKSADNY NKFLTLGNYY AYGIARSSLW ALGIDNSFPL LHGSTRRGGL VF DVADIIK TSIILPLAFH AADQGMSNTE FKRSCVAYFD KNDILAYLIN NIKRLCME

UniProtKB: Cas1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30241
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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