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- EMDB-75685: Effector complex from type IV-C CRISPR-Cas system -

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Basic information

Entry
Database: EMDB / ID: EMD-75685
TitleEffector complex from type IV-C CRISPR-Cas system
Map datahalf map A
Sample
  • Complex: Effector complex from type IV-C CRISPR-Cas system
    • Protein or peptide: Cas10IVc
    • Protein or peptide: Cas5c
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas11c
    • RNA: crRNA (47-MER)
    • DNA: DNA (30-MER)
  • 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: 3.37 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 / Chu X / 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: Cell Rep / Year: 2026
Title: Type IV-C CRISPR-Cas effector complexes recognize double-stranded DNA and switch on collateral cleavage of ssDNA and RNA.
Authors: Conor C Pittman / Chengtao Xu / Ryan J Catchpole / Sandra Garrett / Ryan Fuchs / Xiaomeng Chu / Kira S Makarova / Eugene V Koonin / Peng Zhao / Lance Wells / Brenton R Graveley / Ailong Ke / Michael P Terns /
Abstract: Type IV-C CRISPR-Cas systems remain enigmatic compared to other class 1 systems. Here, we expand the type IV-C catalog, identifying two phylogenetically distinct clades primarily found in archaea (IV- ...Type IV-C CRISPR-Cas systems remain enigmatic compared to other class 1 systems. Here, we expand the type IV-C catalog, identifying two phylogenetically distinct clades primarily found in archaea (IV-C1) or bacteria (IV-C2), distinguishable by the Cas10IVc subunit architecture. We functionally and structurally characterize type IV-C1 systems from Thermococcus onnurineus (Ton) and Pyrococcus abyssi (Pab). Type IV-C complexes assemble with crRNAs derived from distinct CRISPR arrays and recognize a 5'-GGG-3' protospacer adjacent motif (PAM) to bind double-stranded DNA targets. Target recognition activates the HD domain of Cas10IVc, triggering metal-dependent collateral cleavage of single-stranded DNA and RNA. This behavior is explained by allosteric alignment of the HD active site, triggered by PAM-dependent R-loop formation, as revealed by cryo-EM. Together, our findings suggest that type IV-C systems provide immunity via non-specific cleavage of nucleic acids generated during mobile genetic element replication or transcription.
History
DepositionFeb 23, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75685.png

Downloads & links

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Map

FileDownload / File: emd_75685.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf map A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 Å		1.07 Å/pix.
x 512 pix.
= 547.84 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: 0.1
Minimum - Maximum-0.35693315 - 0.89612204
Average (Standard dev.)-0.0004507893 (±0.016840471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 547.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_75685_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_75685_half_map_2.map
Annotationhalf map A
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: Cas5c
    • Protein or peptide: Cas7c
    • Protein or peptide: Cas11c
    • RNA: crRNA (47-MER)
    • DNA: DNA (30-MER)
  • 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-#6
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: Cas5c

MacromoleculeName: Cas5c / type: protein_or_peptide / ID: 2 / 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 #3: Cas7c

MacromoleculeName: Cas7c / type: protein_or_peptide / ID: 3 / 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 #4: Cas11c

MacromoleculeName: Cas11c / type: protein_or_peptide / ID: 4 / 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 #5: crRNA (47-MER)

MacromoleculeName: crRNA (47-MER) / type: rna / ID: 5 / 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 #6: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pyrococcus abyssi (archaea)
Molecular weightTheoretical: 9.232035 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DA)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DA) (DA)(DT)(DT)(DG)(DT)(DA)(DA)(DA)(DT) (DA)

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / 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: 1867493
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66734
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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