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- EMDB-61436: Structure of LaTranC complex bound to 27nt complementary DNA subs... -

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Basic information

Entry
Database: EMDB / ID: EMD-61436
TitleStructure of LaTranC complex bound to 27nt complementary DNA substrate, conformation 2
Map dataLaTraC complex conformational 2 (27nt matched)
Sample
  • Complex: LaTranC
    • Protein or peptide: LaTranC
    • DNA: DNA (42-MER)
    • RNA: RNA (195-MER)
    • DNA: DNA (42-MER)
KeywordsLaTranC CRISPR RNA complex / DNA / gene editing / IMMUNE SYSTEM/DNA/RNA / IMMUNE SYSTEM-DNA-RNA complex
Biological speciesLawsonibacter sp. (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsZhang S / Liu J
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32201224 China
National Natural Science Foundation of China (NSFC)32230088 China
National Natural Science Foundation of China (NSFC)32250012 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, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61436.png

Downloads & links

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Map

FileDownload / File: emd_61436.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLaTraC complex conformational 2 (27nt matched)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-1.9743583 - 3.5281818
Average (Standard dev.)-0.00035633123 (±0.04129467)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: LaTraC complex conformational 2 (27nt matched)

Fileemd_61436_half_map_1.map
AnnotationLaTraC complex conformational 2 (27nt matched)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: LaTraC complex conformational 2 (27nt matched)

Fileemd_61436_half_map_2.map
AnnotationLaTraC complex conformational 2 (27nt matched)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : LaTranC

EntireName: LaTranC
Components
  • Complex: LaTranC
    • Protein or peptide: LaTranC
    • DNA: DNA (42-MER)
    • RNA: RNA (195-MER)
    • DNA: DNA (42-MER)

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Supramolecule #1: LaTranC

SupramoleculeName: LaTranC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / Details: LaTraC complex (27-nt matched) conformation 2
Source (natural)Organism: Lawsonibacter sp. (bacteria)

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Macromolecule #1: LaTranC

MacromoleculeName: LaTranC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lawsonibacter sp. (bacteria)
Molecular weightTheoretical: 64.660348 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString: MSVSFSLNAK KIRLENYAMK MRLYPSPTQA EQMDKMFLAL RLAYNMTFHE VFQQNPAVCG DPDEDGNVWP SYKKMANKTW RKALIDQNP AIAEAPAAAI TTNNGLFLSN GQKAWKTGMH NLPANKADRK DFRFYSLSKP RRSFAVQIPP DCIIPSDTNQ K VARIKLPK ...String:
MSVSFSLNAK KIRLENYAMK MRLYPSPTQA EQMDKMFLAL RLAYNMTFHE VFQQNPAVCG DPDEDGNVWP SYKKMANKTW RKALIDQNP AIAEAPAAAI TTNNGLFLSN GQKAWKTGMH NLPANKADRK DFRFYSLSKP RRSFAVQIPP DCIIPSDTNQ K VARIKLPK IDGAIKARGF NRKIWFGPDG KHTYEEALAA HELSNNLTVR VSKDTCGDYF ICITFSQGKV KGDKPTWEFY QE VRVSPIP EPIGLDVGIK DIAILNTGTK YENKQFKRDR AATLKKMSRQ LSRRWGPANS AFRDYNKNIR AENRALEKAQ QDP GSSGVG PEAPVLKSVA QPSRRYLTIQ KNRAKLERKI ARRRDTYYHQ VTAEVAGKSS LLAVETLRVK NMLQNHRLAF ALSD AAMSD FISKLKYKAR RIQVPLVAIG TFQPSSQTCS VCGSINPAVK NLSIRVWTCP NCGTRHNRDI NAAKNILAIA QNMLE KKVP FADEALPDEK PPAAPVKKAA RKPRDAVFPD HPDLVIRFSK ELTQLNDPRY VIVNKATNQI VDNAQGAGYR SAAKAK NCY KAKLAWSSKT NK

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Macromolecule #2: DNA (42-MER)

MacromoleculeName: DNA (42-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lawsonibacter sp. (bacteria)
Molecular weightTheoretical: 12.84125 KDa
SequenceString:
(DG)(DG)(DA)(DT)(DC)(DC)(DT)(DA)(DA)(DC) (DG)(DT)(DA)(DA)(DG)(DT)(DC)(DC)(DC)(DT) (DC)(DC)(DT)(DA)(DC)(DT)(DG)(DT)(DG) (DT)(DT)(DT)(DG)(DA)(DA)(DA)(DA)(DT)(DC) (DC) (DC)(DG)

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Macromolecule #4: DNA (42-MER)

MacromoleculeName: DNA (42-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Lawsonibacter sp. (bacteria)
Molecular weightTheoretical: 13.02839 KDa
SequenceString:
(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DT)(DT)(DC) (DA)(DA)(DA)(DC)(DA)(DC)(DA)(DG)(DT)(DA) (DG)(DG)(DA)(DG)(DG)(DG)(DA)(DA)(DA) (DG)(DT)(DT)(DG)(DT)(DC)(DC)(DA)(DG)(DA) (DT) (DC)(DC)

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Macromolecule #3: RNA (195-MER)

MacromoleculeName: RNA (195-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Lawsonibacter sp. (bacteria)
Molecular weightTheoretical: 62.94843 KDa
SequenceString: GGUGGGAGGU CUGUCCCCAC CAUGGGGUGC GAACCUUGUG UGCUCAUCAU UGCCGUGAGC GUUCGCACGU CCAAACGACC AUAUCAUCG UUGCCCUGCG ACCAUUCAGC GGCAAUCAAG ACGCAGGCAU GAUAUGUAAC CAUGCAUUGG AAAGUGCAUG G AGCAGAAG ...String:
GGUGGGAGGU CUGUCCCCAC CAUGGGGUGC GAACCUUGUG UGCUCAUCAU UGCCGUGAGC GUUCGCACGU CCAAACGACC AUAUCAUCG UUGCCCUGCG ACCAUUCAGC GGCAAUCAAG ACGCAGGCAU GAUAUGUAAC CAUGCAUUGG AAAGUGCAUG G AGCAGAAG AAACACAGUA GGAGGGACUU ACGUUAG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2448326
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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