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- PDB-9hm4: Structure of tRNA bound Ba1Cas12a3 -

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Basic information

Entry
Database: PDB / ID: 9hm4
TitleStructure of tRNA bound Ba1Cas12a3
Components
  • Ala tRNA
  • Ba1Cas12a3
  • crRNA
  • targetRNA
KeywordsRNA BINDING PROTEIN / crispar-cas nuclease
Function / homology: / RNA / RNA (> 10) / :
Function and homology information
Biological speciesBacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Escherichia coli (E. coli)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYuan, B. / Heinz, D.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: Structure of tRNA bound Ba1Cas12a3
Authors: Yuan, B. / Heinz, D.W.
History
DepositionDec 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 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: Ba1Cas12a3
B: crRNA
C: targetRNA
D: Ala tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,9816
Polymers193,9334
Non-polymers492
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 Ba1Cas12a3


Mass: 135303.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Gene: CVT95_05895 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N2ZXC5
#2: RNA chain crRNA


Mass: 20859.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain targetRNA


Mass: 13292.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain Ala tRNA


Mass: 24476.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA (Ala) / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1845258627
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: tRNA bound Ba1Cas12a3 / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Bacteroidetes bacterium HGW-Bacteroidetes-12 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5 / Details: 50mM TrisHCl 50mM NaCl 1mM DTT 5% glycerol
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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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: 2500 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116277 / Symmetry type: POINT

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