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- EMDB-75667: Effector complex from type IV-C CRISPR-Cas system -

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Basic information

Entry
Database: EMDB / ID: EMD-75667
TitleEffector complex from type IV-C CRISPR-Cas system
Map data
Sample
  • Complex: Effector complex from type IV-C CRISPR-Cas system
    • Protein or peptide: Cas10IVc
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas5c
    • DNA: Non-Target Strand DNA
    • DNA: Target Strand DNA
    • RNA: crRNA (47-MER)
    • Protein or peptide: Cas11c
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsCRISPR-Cas / nuclease / RNA-guided / Cas10 / Cas7 / RNA BINDING PROTEIN
Biological speciesPyrococcus abyssi (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B ...Pittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B / Ke A / Terns M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35118174 United States
CitationJournal: To Be Published
Title: Type IV-C CRISPR-Cas effector complex recognizes double-stranded DNA and switches on collateral cleavage of ssDNA and RNA
Authors: Pittman C / Xu C / Catchpole R / Garrett S / Fuchs R / Makarova K / Koonin E / Zhao P / Wells L / Graveley B / Ke A / Terns M
History
DepositionFeb 21, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75667.png

Downloads & links

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Map

FileDownload / File: emd_75667.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å		1.07 Å/pix.
x 384 pix.
= 410.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.37825364 - 0.9694271
Average (Standard dev.)0.000151461 (±0.0213947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_75667_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_75667_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 : Effector complex from type IV-C CRISPR-Cas system

EntireName: Effector complex from type IV-C CRISPR-Cas system
Components
  • Complex: Effector complex from type IV-C CRISPR-Cas system
    • Protein or peptide: Cas10IVc
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas5c
    • DNA: Non-Target Strand DNA
    • DNA: Target Strand DNA
    • RNA: crRNA (47-MER)
    • Protein or peptide: Cas11c
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Effector complex from type IV-C CRISPR-Cas system

SupramoleculeName: Effector complex from type IV-C CRISPR-Cas system / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Pyrococcus abyssi (archaea)

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Macromolecule #1: Cas10IVc

MacromoleculeName: Cas10IVc / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 70.278211 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEIGREKTL NEFITIKRNS RKSKDKSTIS PRIQKVQMLS QESSFALIKG TIARTDPASG LPHLDELTHH LIAVSSASLK FSSGEIALA ALIHDYYKPV FDFRWNTQKN RWEWYHYITD QKTYSQLLSE FNDSINVSKV ASISKEHHKK GKCNEICQIE Q KSKLISAL ...String:
MKEIGREKTL NEFITIKRNS RKSKDKSTIS PRIQKVQMLS QESSFALIKG TIARTDPASG LPHLDELTHH LIAVSSASLK FSSGEIALA ALIHDYYKPV FDFRWNTQKN RWEWYHYITD QKTYSQLLSE FNDSINVSKV ASISKEHHKK GKCNEICQIE Q KSKLISAL ETSLPFTLPQ RDNYVIVQHL RVPGKYRMFL LALLKEMLSK ELSSRYSKRF QEILGISRIR YEYRPISDLE RT GDKRIED VERIIQKNDW KIEIKENTMI IPLPSKFHKE VFYFEYYEGS EIVLDIDTKA RMIRGVKVPF GMALSTVYFA GAQ DAYLVY VDAGNGLLPL DTLLGTLIED LKRSLSKDKQ ETAFNSIDIS KIVRSLTGKF KSDAMCVFCG EPGEPISNNE KVKR IMEDK FTDTWLLLTH GASVCPACKL GFEIEELFRA KGMNKYLAEE AILKMHLIST DVPIFRSENF LRSISSKIWL ELLSE VYYS LHRSKELQKI TKKNEWATAF YLNPKVIIYP YIADMTPQVL SVTLRYSNKK FVLQSGIHSR VVFPGEEKDM TFEEFR IVR KFYSSHPTTG SNLVKRIRSV YNPIFGVPKV DIQKGGGSRA RKRKN

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Macromolecule #2: Cas7c

MacromoleculeName: Cas7c / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 36.531379 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRVVLKIKAL EPISVGYESI GIETLLYSLP IIKEDGTALE VPVIPGNSLR GVLRDKMALQ FLEDVKSVLI GSKQGSLEAH IGTLLSLFS GGILSGKEKD QSTPNIKEIM EKYVYPLLPL SIMGVALKKI IIPGKIKVGI GYPVTKETKS LLTDLGVPFD E SAPTLSEI ...String:
MRVVLKIKAL EPISVGYESI GIETLLYSLP IIKEDGTALE VPVIPGNSLR GVLRDKMALQ FLEDVKSVLI GSKQGSLEAH IGTLLSLFS GGILSGKEKD QSTPNIKEIM EKYVYPLLPL SIMGVALKKI IIPGKIKVGI GYPVTKETKS LLTDLGVPFD E SAPTLSEI ISSVLITRKD DMNKVMQLKE LLNVQGKVEE VKAGDSAVQQ RLYRQVVVPG TVFYSYVEDI IPMTEAEWGL VL KTLEHLD KIGGRVAGGL GKVKIELHGI NKERKENFIH AYENYIRDNI TDIQEALKKS PNDFFRGSSK SRENVEIDEK AQG RKEPKD SPEA

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Macromolecule #3: Cas5c

MacromoleculeName: Cas5c / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 35.403852 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYLVTLRFRT YPLFLSLSNP NELSQELTPL DGPLAFAEYY RTRLSNDPDW RVKYLEDILT ARKLEWISDI RSSYLLPCTV NKETLTITT PMGFKAVFNV DEKKEAHYKF SEGQPLKKWE SSQIFLRLGR RDDIIKVEIL RNSLGVRLTK KTKGLPSSHS G SYKAVDYS ...String:
MYLVTLRFRT YPLFLSLSNP NELSQELTPL DGPLAFAEYY RTRLSNDPDW RVKYLEDILT ARKLEWISDI RSSYLLPCTV NKETLTITT PMGFKAVFNV DEKKEAHYKF SEGQPLKKWE SSQIFLRLGR RDDIIKVEIL RNSLGVRLTK KTKGLPSSHS G SYKAVDYS LRLYTPNLMW ASVVNGISQR KLDELLRILG KFGIGKKRNM GWGDLLDYQI YELKGENITP DYILHKRGES RF LETWRPI SPEKIAEMIT KSPKGVKLYL LDSKIGYGAD RPPYWRRNLV VKSALFLVQN NNGTTGNVS

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Macromolecule #7: Cas11c

MacromoleculeName: Cas11c / type: protein_or_peptide / ID: 7 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 14.065316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIYKKEVAPV QEKEKIEDLV VSLLGAIDGI IDWGSMGEKV HRKKYSILAK RIAVVAKSSN SLDEFVEKLL SQVAGDSLFI SREKGENFK EVYRKAKEHE GEVLKFLKAY PYLSTVLYAA YVESI

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Macromolecule #4: Non-Target Strand DNA

MacromoleculeName: Non-Target Strand DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 2.981944 KDa
SequenceString:
(DG)(DC)(DC)(DG)(DT)(DG)(DC)(DC)(DC)(DC)

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Macromolecule #5: Target Strand DNA

MacromoleculeName: Target Strand DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 14.600312 KDa
SequenceString:
(DT)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DT)(DG) (DC)(DG)(DG)(DT)(DC)(DC)(DT)(DT)(DG)(DC) (DG)(DG)(DC)(DT)(DG)(DA)(DG)(DA)(DG) (DC)(DA)(DC)(DT)(DT)(DC)(DA)(DG)(DG)(DG) (DG) (DC)(DA)(DC)(DG)(DG)(DC)(DG)

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Macromolecule #6: crRNA (47-MER)

MacromoleculeName: crRNA (47-MER) / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 15.131104 KDa
SequenceString:
AUUGAAAGCU GAAGUGCUCU CAGCCGCAAG GACCGCAUAC UACAAGA

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 883889
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41573
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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