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- PDB-9ebu: Wild-type EsCas13d binary complex -

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Basic information

Entry
Database: PDB / ID: 9ebu
TitleWild-type EsCas13d binary complex
Components
  • EsCas13d
  • crRNA
KeywordsRNA BINDING PROTEIN/RNA / Cas13 / CRISPR / HEPN / RNA nuclease / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10) / Uncharacterized protein
Function and homology information
Biological species[Eubacterium] siraeum DSM 15702 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsChou, C.W. / Finkelstein, I.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-1808 United States
CitationJournal: To Be Published
Title: Structural Basis for Target Discrimination and Activation by Cas13d
Authors: Chou, C.W. / Finkelstein, I.J.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 19, 2025Data 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: EsCas13d
B: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,5923
Polymers127,5682
Non-polymers241
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 EsCas13d


Mass: 110828.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] siraeum DSM 15702 (bacteria)
Gene: EUBSIR_02687 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B0MS50
#2: RNA chain crRNA


Mass: 16739.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] siraeum DSM 15702 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: The active state of EsCas13d protein with crRNA and matched target
Type: COMPLEX / Entity ID: #2, #1 / Source: NATURAL
Molecular weightValue: 0.135 MDa / Experimental value: NO
Source (natural)Organism: [Eubacterium] siraeum DSM 15702 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.135 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Image recordingElectron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192389 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 46.15 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00488339
ELECTRON MICROSCOPYf_angle_d0.61411459
ELECTRON MICROSCOPYf_chiral_restr0.04181304
ELECTRON MICROSCOPYf_plane_restr0.00361285
ELECTRON MICROSCOPYf_dihedral_angle_d15.39781662

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