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- EMDB-36830: ICP1 Csy-dsDNA complex (partial duplex) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-36830
TitleICP1 Csy-dsDNA complex (partial duplex)
Map data
Sample
  • Complex: csy complex
    • Protein or peptide: Csy4
    • Protein or peptide: Csy1
    • Protein or peptide: Csy2
    • Protein or peptide: Csy3
  • RNA: RNA (60-MER)
  • DNA: DNA (49-MER)
  • DNA: DNA (25-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: 3.6 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-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36830.png

Downloads & links

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Map

FileDownload / File: emd_36830.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.07337161 - 0.13008791
Average (Standard dev.)0.00048584925 (±0.0043834588)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 233.28001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_36830_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36830_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: Csy4
    • Protein or peptide: Csy1
    • Protein or peptide: Csy2
    • Protein or peptide: Csy3
  • RNA: RNA (60-MER)
  • DNA: DNA (49-MER)
  • DNA: DNA (25-MER)

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Supramolecule #1: csy complex

SupramoleculeName: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #7, #1-#3
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 #7: Csy4

MacromoleculeName: Csy4 / type: protein_or_peptide / ID: 7 / 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 #4: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 19.046227 KDa
SequenceString:
CUUAAAGAGU CAACCCUUUG CUUAUCUUCC CUAUUUAAAU GUUAGCAGCC GCAUAGGCUG

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Macromolecule #5: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 15.193796 KDa
SequenceString:
(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DT)(DA)(DG) (DG)(DG)(DA)(DA)(DG)(DA)(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 (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 7.712994 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)

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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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 240070
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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