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- PDB-11fs: Effector complex from type IV-C CRISPR-Cas system -

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Basic information

Entry
Database: PDB / ID: 11fs
TitleEffector complex from type IV-C CRISPR-Cas system
Components
  • Cas10IVc
  • Cas11c
  • Cas5c
  • Cas7c
  • Non-Target Strand DNA
  • Target Strand DNA
  • crRNA (47-MER)
KeywordsRNA BINDING PROTEIN / CRISPR-Cas / nuclease / RNA-guided / Cas10 / Cas7
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesPyrococcus abyssi (archaea)
MethodELECTRON MICROSCOPY / single 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, 1items
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, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas10IVc
C: Cas7c
D: Cas5c
E: Non-Target Strand DNA
F: Target Strand DNA
G: crRNA (47-MER)
H: Cas7c
I: Cas7c
J: Cas7c
K: Cas7c
L: Cas7c
M: Cas7c
N: Cas11c
O: Cas11c
P: Cas11c
Q: Cas11c
R: Cas11c
S: Cas11c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,62121
Polymers478,50718
Non-polymers1143
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 15 molecules ACHIJKLMDNOPQRS

#1: Protein Cas10IVc


Mass: 70278.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)
#2: Protein
Cas7c


Mass: 36531.379 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)
#3: Protein Cas5c


Mass: 35403.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)
#7: Protein
Cas11c


Mass: 14065.316 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)

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DNA chain , 2 types, 2 molecules EF

#4: DNA chain Non-Target Strand DNA


Mass: 2981.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi (archaea)
#5: DNA chain Target Strand DNA


Mass: 14600.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi (archaea)

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RNA chain , 1 types, 1 molecules G

#6: RNA chain crRNA (47-MER)


Mass: 15131.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Effector complex from type IV-C CRISPR-Cas system / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Pyrococcus abyssi (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 883889
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41573 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00231295
ELECTRON MICROSCOPYf_angle_d0.46742668
ELECTRON MICROSCOPYf_dihedral_angle_d15.7395126
ELECTRON MICROSCOPYf_chiral_restr0.0414958
ELECTRON MICROSCOPYf_plane_restr0.0034955

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