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- PDB-9jfp: Structure of LaTranC complex bound to 6nt complementary DNA substrate -

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Basic information

Entry
Database: PDB / ID: 9jfp
TitleStructure of LaTranC complex bound to 6nt complementary DNA substrate
Components
  • (DNA (37-MER)) x 2
  • LaTranC
  • RNA (195-MER)
KeywordsIMMUNE SYSTEM/DNA/RNA / LaTranC complexes / IMMUNE SYSTEM-DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLawsonibacter sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsZhang, S. / Liu, J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201224 China
National Natural Science Foundation of China (NSFC)32250012 China
National Natural Science Foundation of China (NSFC)32230088 China
National Natural Science Foundation of China (NSFC)32201224 China
CitationJournal: Cell / Year: 2025
Title: Functional RNA splitting drove the evolutionary emergence of type V CRISPR-Cas systems from transposons.
Authors: Shuai Jin / Zixu Zhu / Yunjia Li / Shouyue Zhang / Yijing Liu / Danyuan Li / Yuanqing Li / Yingfeng Luo / Zhiheng Cheng / Kevin Tianmeng Zhao / Qiang Gao / Guanglei Yang / Hongchao Li / ...Authors: Shuai Jin / Zixu Zhu / Yunjia Li / Shouyue Zhang / Yijing Liu / Danyuan Li / Yuanqing Li / Yingfeng Luo / Zhiheng Cheng / Kevin Tianmeng Zhao / Qiang Gao / Guanglei Yang / Hongchao Li / Ronghong Liang / Rui Zhang / Jin-Long Qiu / Yong E Zhang / Jun-Jie Gogo Liu / Caixia Gao /
Abstract: Transposon-encoded TnpB nucleases gave rise to type V CRISPR-Cas12 effectors through multiple independent domestication events. These systems use different RNA molecules as guides for DNA targeting: ...Transposon-encoded TnpB nucleases gave rise to type V CRISPR-Cas12 effectors through multiple independent domestication events. These systems use different RNA molecules as guides for DNA targeting: transposon-derived right-end RNAs (reRNAs or omega RNAs) for TnpB and CRISPR RNAs for type V CRISPR-Cas systems. However, the molecular mechanisms bridging transposon activity and CRISPR immunity remain unclear. We identify TranCs (transposon-CRISPR intermediates) derived from distinct IS605- or IS607-TnpB lineages. TranCs utilize both CRISPR RNAs and reRNAs to direct DNA cleavage. The cryoelectron microscopy (cryo-EM) structure of LaTranC from Lawsonibacter sp. closely resembles that of the ISDra2 TnpB complex; however, unlike a single-molecule reRNA, the LaTranC guide RNA is functionally split into a tracrRNA and crRNA. An engineered RNA split of ISDra2 TnpB enabled activity with a CRISPR array. These findings indicate that functional RNA splitting was the primary molecular event driving the emergence of diverse type V CRISPR-Cas systems from transposons.
History
DepositionSep 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.1Nov 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (37-MER)
D: DNA (37-MER)
F: RNA (195-MER)
A: LaTranC


Theoretical massNumber of molelcules
Total (without water)139,6824
Polymers139,6824
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: DNA chain DNA (37-MER)


Mass: 11404.304 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lawsonibacter sp. (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: DNA chain DNA (37-MER)


Mass: 11383.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lawsonibacter sp. (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#3: RNA chain RNA (195-MER)


Mass: 62948.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lawsonibacter sp. (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#4: Protein LaTranC


Mass: 53946.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lawsonibacter sp. (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
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: LaTranC / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Lawsonibacter sp. (bacteria)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3229410 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037404
ELECTRON MICROSCOPYf_angle_d0.56710785
ELECTRON MICROSCOPYf_dihedral_angle_d20.8372368
ELECTRON MICROSCOPYf_chiral_restr0.0341298
ELECTRON MICROSCOPYf_plane_restr0.004779

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