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- PDB-21kl: Cryo-EM structure of TasH-pre-tigRNA-dsDNA complex -

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Basic information

Entry
Database: PDB / ID: 21kl
TitleCryo-EM structure of TasH-pre-tigRNA-dsDNA complex
Components
  • (DNA (38-MER)) x 2
  • RNA (37-MER)
  • putative nuclease
KeywordsANTIVAL PROTEIN/RNA/DNA / protein complex / ANTIVIRAL PROTEIN/RNA/DNA / ANTIVAL PROTEIN-RNA-DNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesSalicola phage CGphi29 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsZhang, H. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Mol Cell / Year: 2026
Title: Molecular basis for dual-spacer-guided target cleavage by the TIGR-TasH system.
Authors: Jie Yang / Tongyao Wang / Zhikun Liu / Wenqi Wu / Yangyue Sun / Yancheng Zhan / Shuqin Zhang / Hong Chen / Bin Liu / Caidie Yue / Zhenning Yin / Zhengda Shan / Xuzichao Li / Zhuang Li / ...Authors: Jie Yang / Tongyao Wang / Zhikun Liu / Wenqi Wu / Yangyue Sun / Yancheng Zhan / Shuqin Zhang / Hong Chen / Bin Liu / Caidie Yue / Zhenning Yin / Zhengda Shan / Xuzichao Li / Zhuang Li / Zhiyong Yuan / Hang Yin / Heng Zhang /
Abstract: The RNA-directed programmable nuclease systems, exemplified by the CRISPR-Cas system, have been widely used in genome editing. In contrast to the single-spacer configuration of CRISPR RNA (crRNA), ...The RNA-directed programmable nuclease systems, exemplified by the CRISPR-Cas system, have been widely used in genome editing. In contrast to the single-spacer configuration of CRISPR RNA (crRNA), the guide RNA (tigRNA) of the tandem interspaced guide RNA (TIGR) system features a dual-spacer arrangement, thereby directing the TIGR-associated (Tas) protein to engage both strands of the target double-stranded DNA (dsDNA). Here, we determine six cryo-electron microscopy structures of the Salicola phage TIGR-TasH complex. The central coiled-coil region of TasH mediates dimerization, while the C-terminal nucleolar protein (Nop) domain is able to autonomously process precursor tigRNA. Upon target binding, the dynamic N-terminal HNH nuclease domain is recruited for cleavage through a β-hairpin, which also determines the target preference. More interestingly, the conserved box C motif of tigRNA stabilizes this β-hairpin in an adenine-specific manner, enabling us to rationally design a guide RNA-defined nickase, distinct from conventional protein-based nickase strategies used in genome editing.
History
DepositionDec 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative nuclease
B: putative nuclease
C: RNA (37-MER)
D: DNA (38-MER)
E: DNA (38-MER)


Theoretical massNumber of molelcules
Total (without water)115,4025
Polymers115,4025
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein putative nuclease


Mass: 40031.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salicola phage CGphi29 (virus) / Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (37-MER)


Mass: 11948.239 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salicola phage CGphi29 (virus) / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA (38-MER)


Mass: 11606.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salicola phage CGphi29 (virus) / Production host: Escherichia coli (E. coli)
#4: DNA chain DNA (38-MER)


Mass: 11784.576 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salicola phage CGphi29 (virus) / 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: putative nuclease / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salicola phage CGphi29 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
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: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107720 / Symmetry type: POINT

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