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- PDB-8xca: Cryo-EM structure of Cas12o1, crRNA and target DNA complex -

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Open data


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Basic information

Entry
Database: PDB / ID: 8xca
TitleCryo-EM structure of Cas12o1, crRNA and target DNA complex
Components
  • CasJ19
  • CrRNA
  • DNA (5'-D(P*AP*CP*GP*AP*TP*AP*TP*G)-3')
  • TS-DNA
KeywordsRNA BINDING PROTEIN/RNA/DNA / Crispr-Cas protein / RNA BINDING PROTEIN-RNA-DNA COMPLEX
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
unclassified sequences (unknown)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell Res / Year: 2025
Title: Structure and genome editing activity of the novel CRISPR-Cas12o1 effector.
Authors: Zhiqiang Duan / Xi Zhang / Jun-Tao Zhang / Xingkun Ji / Ruiheng Liu / Ying Chen / Shanshan Li / Nannan Jia / Huizhi Gao / Yu Xin / Ning Jia / Jian-Kang Zhu /
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / em_admin / em_author_list / pdbx_contact_author / struct
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update / _em_admin.title / _em_author_list.author / _pdbx_contact_author.name_first / _pdbx_contact_author.name_last / _struct.title
Revision 1.2Aug 20, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CasJ19
B: CrRNA
C: TS-DNA
D: DNA (5'-D(P*AP*CP*GP*AP*TP*AP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)151,9014
Polymers151,9014
Non-polymers00
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 CasJ19


Mass: 105573.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: RNA chain CrRNA


Mass: 19229.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified sequences (unknown) / Production host: unclassified sequences (unknown)
#3: DNA chain TS-DNA


Mass: 13644.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified sequences (unknown) / Production host: unclassified sequences (unknown)
#4: DNA chain DNA (5'-D(P*AP*CP*GP*AP*TP*AP*TP*G)-3')


Mass: 13453.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified sequences (unknown) / Production host: unclassified sequences (unknown)
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: Ternary complex of Cas12J19, CrRNA and target DNA complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: unidentified (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91967 / Symmetry type: POINT

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