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- EMDB-36831: ICP1 Csy-dsDNA complex (form 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-36831
TitleICP1 Csy-dsDNA complex (form 1)
Map data
Sample
  • Complex: csy complex
    • Protein or peptide: Csy1
    • Protein or peptide: Csy2
    • Protein or peptide: Csy3
    • Protein or peptide: Csy4
    • DNA: DNA (33-MER)
    • DNA: DNA (27-MER)
    • RNA: RNA (59-MER)
KeywordsIMMUNE SYSTEM-RNA-DNA complex / RNA BINDING PROTEIN/DNA/RNA / 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
Csy4 / Csy3 / Csy2 / Csy1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZhang LX / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: Nat Chem Biol / Year: 2024
Title: Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system.
Authors: Laixing Zhang / Hao Wang / Jianwei Zeng / Xueli Cao / Zhengyu Gao / Zihe Liu / Feixue Li / Jiawei Wang / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, ...Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are prokaryotic adaptive immune systems against invading phages and other mobile genetic elements. Notably, some phages, including the Vibrio cholerae-infecting ICP1 (International Center for Diarrheal Disease Research, Bangladesh cholera phage 1), harbor CRISPR-Cas systems to counteract host defenses. Nevertheless, ICP1 Cas8f lacks the helical bundle domain essential for recruitment of helicase-nuclease Cas2/3 during target DNA cleavage and how this system accomplishes the interference stage remains unknown. Here, we found that Cas1, a highly conserved component known to exclusively work in the adaptation stage, also mediates the interference stage through connecting Cas2/3 to the DNA-bound CRISPR-associated complex for antiviral defense (Cascade; CRISPR system yersinia, Csy) of the ICP1 CRISPR-Cas system. A series of structures of Csy, Csy-dsDNA (double-stranded DNA), Cas1-Cas2/3 and Csy-dsDNA-Cas1-Cas2/3 complexes reveal the whole process of Cas1-mediated target DNA cleavage by the ICP1 CRISPR-Cas system. Together, these data support an unprecedented model in which Cas1 mediates the interference stage in a phage-encoded CRISPR-Cas system and the study also sheds light on a unique model of primed adaptation.
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36831.png

Downloads & links

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Map

FileDownload / File: emd_36831.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: 0.2
Minimum - Maximum-1.6780262 - 2.751438
Average (Standard dev.)0.0074559 (±0.083347164)
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_36831_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_36831_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
    • Protein or peptide: Csy1
    • Protein or peptide: Csy2
    • Protein or peptide: Csy3
    • Protein or peptide: Csy4
    • DNA: DNA (33-MER)
    • DNA: DNA (27-MER)
    • RNA: RNA (59-MER)

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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: Csy1

MacromoleculeName: Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 20.409918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIKEMIEDFI SKGGLIFTHS GRYTNTNNSC FIFNKNDIGV DTKVDMYTPK SAGIKNEEGE NLWQVLNKAN MFYRIYSGEL GEELQYLLK SCCTAKEDVT TLPQIYFKNG EGYDILVPIG NAHNLISGTE YLWEHKYYNT FTQKLGGSNP QNCTHACNKM R GGFKQFNC TPPQVEDNYN A

UniProtKB: Csy1

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Macromolecule #2: Csy2

MacromoleculeName: Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 27.401547 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRKFIIVKNV KVDGINAKSS DITVGMPPAT TFCGLGETMS IKTGIVVKAV SYGSVKFEVR GSRFNTSVTK FAWQDRGNGG KANNNSPIQ PKPLADGVFT LCFEVEWEDC AEVLVDKVTN FINTARIAGG TIASFNKPFV KVAKDAEELA SVKNAMMPCY V VVDCGVEV ...String:
MRKFIIVKNV KVDGINAKSS DITVGMPPAT TFCGLGETMS IKTGIVVKAV SYGSVKFEVR GSRFNTSVTK FAWQDRGNGG KANNNSPIQ PKPLADGVFT LCFEVEWEDC AEVLVDKVTN FINTARIAGG TIASFNKPFV KVAKDAEELA SVKNAMMPCY V VVDCGVEV NIFEDAVNRK LQPMVNGYKK LEKIVDNKHM RDKFTPAYLA TPTYTMIGYK MVSNVDNFDQ ALWQYGENTK VK TIGGIYN D

UniProtKB: Csy2

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Macromolecule #3: Csy3

MacromoleculeName: Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 33.399301 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKLKAPAVL AYSRKINPTN ALMFAVNWSD RDNTTAVMVG TKTVAGTQSV RGNPNDADKG NIQTVNFANL PHNKNTLLVK YNVKFVGDV FKAELGGGEY SNTLQTALEN TDFGTLAYRY VYNIAAGRTL WRNRVGAESI ETVITVNDQT FTFSDLLVNE F DEDVDVAE ...String:
MTKLKAPAVL AYSRKINPTN ALMFAVNWSD RDNTTAVMVG TKTVAGTQSV RGNPNDADKG NIQTVNFANL PHNKNTLLVK YNVKFVGDV FKAELGGGEY SNTLQTALEN TDFGTLAYRY VYNIAAGRTL WRNRVGAESI ETVITVNDQT FTFSDLLVNE F DEDVDVAE IADMVAGVLS GEGFVTLKVE HYMLLGEGSE VFPSQEFVEN SKLSKQLFDL NGQAAMHDQK IGNAIRTIDT WY EDATTPI AVEPYGSVVR NGVAYRAGNK TDLFTLMDGA VNGKSLTEED QMFVTANLIR GGVFGGGKD

UniProtKB: Csy3

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Macromolecule #4: Csy4

MacromoleculeName: Csy4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 18.73668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYNTISITVV DADDVGVNFV VSKVLSTLHN KGIFNGEVGV TFPRMDKNVG DIITLFSKTG VDRKVLTSTL NTLTDFIHIG KPKEADKVK TYRKVDTKSK GKLIRRCIKR KGVSAETAES LYGNYKGEKC KLPYIVVNSK STGQRFSMFL EECENSEKFN S YGLCIVSC

UniProtKB: Csy4

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Macromolecule #5: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 10.154547 KDa
SequenceString:
(DT)(DA)(DA)(DG)(DC)(DA)(DA)(DA)(DG)(DG) (DG)(DT)(DT)(DG)(DA)(DC)(DG)(DA)(DA)(DA) (DG)(DC)(DC)(DC)(DT)(DT)(DT)(DG)(DT) (DC)(DC)(DC)(DT)

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Macromolecule #6: DNA (27-MER)

MacromoleculeName: DNA (27-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 8.330393 KDa
SequenceString:
(DA)(DG)(DG)(DG)(DA)(DC)(DA)(DA)(DA)(DG) (DG)(DG)(DC)(DT)(DT)(DT)(DC)(DC)(DA)(DT) (DT)(DT)(DA)(DT)(DT)(DT)(DA)

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Macromolecule #7: RNA (59-MER)

MacromoleculeName: RNA (59-MER) / type: rna / ID: 7 / Number of copies: 1
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 18.701021 KDa
SequenceString:
CUUAAAGAGU CAACCCUUUG CUUAUCUUCC CUAUUUAAAU GUUAGCAGCC GCAUAGGCU

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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: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90717
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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