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- PDB-8xcc: Cryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex -

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Basic information

Entry
Database: PDB / ID: 8xcc
TitleCryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex
Components
  • Cas12j19(E100K)
  • CrRNA
  • NTS-DNA
  • 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 speciesunclassified sequences (unknown)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXi, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12j19 (E100K), crRNA and target DNA complex
Authors: Xi, Z.
History
DepositionDec 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas12j19(E100K)
B: CrRNA
C: TS-DNA
D: NTS-DNA


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 Cas12j19(E100K)


Mass: 105573.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unclassified sequences (unknown) / 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 NTS-DNA


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(E100K), CrRNA and target DNA complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: unclassified sequences (unknown)
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: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104917 / Symmetry type: POINT

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