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- PDB-9jhd: Cryo-EM structure of RacrIC1-Cascade IC1-complex III -

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Basic information

Entry
Database: PDB / ID: 9jhd
TitleCryo-EM structure of RacrIC1-Cascade IC1-complex III
Components
  • CRISPR-associated protein, CT1133 family
  • CRISPR-associated protein, TM1801 family
  • RacrIC1 (124-MER)
KeywordsRNA BINDING PROTEIN/RNA / complex / anti-CRISPR / Racr / cryo-EM / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements
Similarity search - Function
CRISPR-associated protein Csd2 / CRISPR-associated protein Cas7, subtype I-B/I-C / CRISPR-associated protein Cas7 / CRISPR-associated protein, Csd1-type / CRISPR-associated protein (Cas_Csd1)
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / CRISPR-associated protein, TM1801 family / CRISPR-associated protein, CT1133 family
Similarity search - Component
Biological speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Bifidobacterium pseudocatenulatum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWang, H. / Zhang, S. / Li, S. / Zhang, K. / Feng, Y.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural insights into inhibition of CRISPR-Cas by RNA anti-CRISPRs
Authors: Wang, H. / Zhang, S. / Li, S. / Zhang, K. / Feng, Y.
History
DepositionSep 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein, TM1801 family
B: CRISPR-associated protein, TM1801 family
C: CRISPR-associated protein, TM1801 family
D: CRISPR-associated protein, TM1801 family
E: CRISPR-associated protein, TM1801 family
F: CRISPR-associated protein, TM1801 family
G: CRISPR-associated protein, TM1801 family
H: CRISPR-associated protein, TM1801 family
I: CRISPR-associated protein, TM1801 family
J: CRISPR-associated protein, TM1801 family
K: CRISPR-associated protein, TM1801 family
L: CRISPR-associated protein, CT1133 family
M: CRISPR-associated protein, CT1133 family
N: CRISPR-associated protein, CT1133 family
O: CRISPR-associated protein, CT1133 family
P: CRISPR-associated protein, CT1133 family
Q: CRISPR-associated protein, CT1133 family
R: CRISPR-associated protein, CT1133 family
S: CRISPR-associated protein, CT1133 family
T: RacrIC1 (124-MER)


Theoretical massNumber of molelcules
Total (without water)498,93620
Polymers498,93620
Non-polymers00
Water00
1


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

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Components

#1: Protein
CRISPR-associated protein, TM1801 family / Cas7c subunit of D. vulgaris type I-C Cascade


Mass: 32227.717 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVUA0132 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72WF7
#2: Protein
CRISPR-associated protein, CT1133 family / Cas11c subunit of D. vulgaris type I-C Cascade


Mass: 13072.887 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Gene: DVUA0131 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72WF8
#3: RNA chain RacrIC1 (124-MER)


Mass: 39847.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium pseudocatenulatum (bacteria)
Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: Cryo-EM structure of RacrIC1-Cascade IC1-complex III / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.47 MDa / Experimental value: YES
Source (natural)Organism: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding 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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
12cryoSPARC4.5.1classification
13cryoSPARC4.5.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1677991
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82089 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00633964
ELECTRON MICROSCOPYf_angle_d0.50346180
ELECTRON MICROSCOPYf_dihedral_angle_d11.91412993
ELECTRON MICROSCOPYf_chiral_restr0.0435123
ELECTRON MICROSCOPYf_plane_restr0.0045860

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