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- PDB-8zqh: Cryo-EM structure of Cas12X with crRNA and Target DNA, Conformation 3 -

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Basic information

Entry
Database: PDB / ID: 8zqh
TitleCryo-EM structure of Cas12X with crRNA and Target DNA, Conformation 3
Components
  • (DNA (44-MER)) x 2
  • Cas12X
  • RNA (60-MER)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Crispr-Cas12 / 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: 3.12 Å
AuthorsZhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of Cas12X with crRNA and Target DNA, Conformation 3
Authors: Zhang, X.
History
DepositionJun 3, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 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

Downloads & links

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Assembly

Deposited unit
B: RNA (60-MER)
C: DNA (44-MER)
A: Cas12X
D: DNA (44-MER)


Theoretical massNumber of molelcules
Total (without water)152,7304
Polymers152,7304
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: RNA chain RNA (60-MER)


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)
#2: DNA chain DNA (44-MER)


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)
#3: Protein Cas12X


Mass: 106402.023 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)
#4: DNA chain DNA (44-MER)


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 Cas12X with crRNA and Target DNA / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
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: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88876 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049311
ELECTRON MICROSCOPYf_angle_d0.58712887
ELECTRON MICROSCOPYf_dihedral_angle_d16.2731860
ELECTRON MICROSCOPYf_chiral_restr0.0391425
ELECTRON MICROSCOPYf_plane_restr0.0071410

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