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- EMDB-36826: ICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composi... -

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Basic information

Entry
Database: EMDB / ID: EMD-36826
TitleICP1 Csy-dsDNA-Cas1-Cas2/3 complex (fully assembled form) composited structure with C1 symmetry
Map datathis is a composite map
Sample
  • Complex: csy complex
    • Protein or peptide: x 6 types
    • RNA: x 1 types
    • DNA: x 3 types
  • Ligand: x 1 types
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 / DNA endonuclease activity / endonuclease activity / defense response to virus / hydrolase activity / DNA 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 / 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, YPEST subtype / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / 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
Csy4 / Csy3 / Csy2 / Csy1 / HD Cas3-type domain-containing protein / Cas1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.75 Å
AuthorsZhang LX / Feng Y
Funding support China, 1 items
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 LX / Feng Y
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36826.png

Downloads & links

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Map

FileDownload / File: emd_36826.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is a composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. 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: 0.015
Minimum - Maximum-0.31335562 - 2.5518427
Average (Standard dev.)0.001916899 (±0.027060254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: this is a original map

Fileemd_36826_additional_1.map
Annotationthis is a original map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36826_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_36826_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: Cas1
    • Protein or peptide: Csy3
    • Protein or peptide: Csy4
    • RNA: RNA (60-MER)
    • DNA: DNA (43-MER)
    • DNA: DNA (31-MER)
    • Protein or peptide: HD Cas3-type domain-containing protein
    • 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')
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: csy complex

SupramoleculeName: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 20.224736 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 TPPQVEDNY

UniProtKB: Csy1

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Macromolecule #2: Csy2

MacromoleculeName: Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / 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: Cas1

MacromoleculeName: Cas1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 34.286137 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 NIKRLCMENS DVHQD

UniProtKB: Cas1

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Macromolecule #4: Csy3

MacromoleculeName: Csy3 / type: protein_or_peptide / ID: 4 / Number of copies: 12 / 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 #5: Csy4

MacromoleculeName: Csy4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / 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 #9: HD Cas3-type domain-containing protein

MacromoleculeName: HD Cas3-type domain-containing protein / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 104.703031 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAMSDTGS VPKYTTKKV YKPDDSIFTL KQGLVGVAAL WHDLGKANSY FQRKLRGECN PSDPVRHEWV SGVIVSTFAK GNDWLSDDFI I PEVKHSDN ...String:
MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAMSDTGS VPKYTTKKV YKPDDSIFTL KQGLVGVAAL WHDLGKANSY FQRKLRGECN PSDPVRHEWV SGVIVSTFAK GNDWLSDDFI I PEVKHSDN VFGDDQVLNA VLWLINTHHK KGLVEDPIYR ATKTMFTETL QCVNVNGGWF NYGDNIDECY KIDTSFITDT YV KQLNRYR KKLLATKHIW FTLGEDQKIA ILQECRVALM LGDSNFSSDL IGGDGSHLYA NLDECGNLKQ TLTQHLLGVT DCA LKALFT INHHKPVKAN FIPTIAEKGE GKFAWQNGVN MVDSSIDNMF CINMASTGKG KTLANLKLLQ HFGNVRCSFG LGMV SLTKQ TAKQFLDMGV DYNSAAMVTG FSKSRFNLGS ESLDQDEVSV EYWGQTSSLS KVFPNNNAGF KNKKLLSAPI LVTTT DHLV KASGVKKGNK QMLPYVRCMH SDLVLDEIDD YGIEDMVVLA RLVYLTACYG NKVIISSATI TPAISNIFYE AYSSGY KVF CANKQTTYKG VNVVWWDEFG IKVEKVTDQF SNLNTRFVNK RITNLLESTP KHKALVVDQD DNMEAVKQSI TTLHNAH NS GGVSFGLIRT TTIKDCVAVT QELQNWETDL SIKILCYHSR FVGDTKAQME EYLSKVLNRK GDEYKKFVDT TTPTAYIV V ATPVVEVGRD FDFDWAIIEP SSERSIVQCA GRVLRHRSST PTTHNIHILK YPFKFYRNSN ICYDVAGYES KGYKLKSKN MLDIYKKESI VNSVNRLQGD AAFYTKSLTA LEHKVLLDKL TTDIADTNVF VGGWQLTANP HEYCKWRRGT KNEDLVLTDG KWSGNVTTT KPIQSKIWRK WQGENGSITV PEYLLDKTIC YNDFYGGYEN E

UniProtKB: HD Cas3-type domain-containing protein

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Macromolecule #6: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 6 / Number of copies: 2
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 #7: DNA (43-MER)

MacromoleculeName: DNA (43-MER) / type: dna / ID: 7 / Number of copies: 3 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 13.431698 KDa
SequenceString:
(DA)(DG)(DC)(DA)(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)

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Macromolecule #8: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 8 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 9.346992 KDa
SequenceString:
(DG)(DG)(DC)(DT)(DT)(DT)(DC)(DG)(DT)(DC) (DA)(DA)(DC)(DC)(DC)(DT)(DT)(DT)(DG)(DC) (DT)(DT)(DA)(DT)(DC)(DT)(DT)(DC)(DC) (DC)(DT)

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Macromolecule #10: 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: 10 / 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 #11: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 11 / Number of copies: 4 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 132865
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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