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- PDB-11vq: DNA-guided AsCas12a -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 11vq
TitleDNA-guided AsCas12a
Components
  • CRISPR-associated endonuclease Cas12a
  • Target RNA
  • psiDNA
KeywordsDNA BINDING PROTEIN / CRISPR-Cas12a / psi-DNA / Ternary Complex / Effector / RNA-binding / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / deoxyribonuclease I / deoxyribonuclease I activity
Similarity search - Function
: / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesAcidaminococcus sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsFregoso Ocampo, R. / Taylor, D.W. / Jain, P.K. / Orosco, C. / West, M.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationF-1938 United States
CitationJournal: To Be Published
Title: An intricately folded guide RNA scaffold enables DNA targeting by the compact Cas9d nuclease
Authors: Fregoso Ocampo, R. / Bravo, J. / Das, A. / Nielsen, S. / Taylor, D.W.
History
DepositionMar 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 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: CRISPR-associated endonuclease Cas12a
B: Target RNA
C: psiDNA


Theoretical massNumber of molelcules
Total (without water)176,2413
Polymers176,2413
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 endonuclease Cas12a / AsCpf1 / CRISPR-associated endonuclease Cpf1


Mass: 151418.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. (bacteria) / Gene: cas12a, cpf1, HMPREF1246_0236 / Production host: Escherichia coli (E. coli)
References: UniProt: U2UMQ6, deoxyribonuclease I, Bacillus subtilis ribonuclease
#2: RNA chain Target RNA


Mass: 12216.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. (bacteria) / Production host: Escherichia coli (E. coli)
#3: DNA chain psiDNA


Mass: 12606.116 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. (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: Cas12a:psiDNA:tarRNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.151206 MDa / Experimental value: NO
Source (natural)Organism: Acidaminococcus sp. (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 DE3
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 defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 79 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 296277 / Symmetry type: POINT

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