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- PDB-21wj: BaCas12a3 ternary complex -

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Basic information

Entry
Database: PDB / ID: 21wj
TitleBaCas12a3 ternary complex
Components
  • Nuclease
  • RNA (27-MER)
  • RNA (43-MER)
KeywordsIMMUNE SYSTEM/RNA / Cas12 / Complex / CRISPR-Cas / nuclease / IMMUNE SYSTEM-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesBacteroidales (bacteria)
Bacteroidales bacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsJi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: BaCas12a3 represents a new subtype of type V CRISPR effector
Authors: Ji, S.
History
DepositionDec 31, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 14, 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: Nuclease
B: RNA (43-MER)
C: RNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,0976
Polymers164,9833
Non-polymers1143
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Nuclease


Mass: 138106.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroidales (bacteria) / Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (43-MER)


Mass: 13539.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: crRNA / Source: (gene. exp.) Bacteroidales bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#3: RNA chain RNA (27-MER)


Mass: 13337.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacteroidales bacterium (bacteria)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestY
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: Ternay complex of crRNA and target RNA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Bacteroidales (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationCryogen name: NITROGEN / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 530902 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 120.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004211362
ELECTRON MICROSCOPYf_angle_d0.580215612
ELECTRON MICROSCOPYf_chiral_restr0.03661753
ELECTRON MICROSCOPYf_plane_restr0.00351761
ELECTRON MICROSCOPYf_dihedral_angle_d15.07062238

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