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- EMDB-42941: TnsD-TnsC-DNA complex -

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Basic information

Entry
Database: EMDB / ID: EMD-42941
TitleTnsD-TnsC-DNA complex
Map data
Sample
  • Complex: Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associated transposon system
    • Protein or peptide: TnsC
    • DNA: DNA (41-MER)
    • DNA: DNA (41-MER)
    • Protein or peptide: TnsD
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsTnsC / TnsD / Tn7-like transposon / type I-B2 CAST / DNA BINDING PROTEIN-DNA complex
Function / homology: / AAA domain / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ORC1/DEAH AAA+ ATPase domain-containing protein
Function and homology information
Biological speciesPeltigera membranacea (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsChang L / Wang S
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2024
Title: Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition.
Authors: Shukun Wang / Romana Siddique / Mark C Hall / Phoebe A Rice / Leifu Chang /
Abstract: Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the ...Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the transpososome and facilitate transposition. Although this pathway is well established, atomic-level structural insights of this process remain largely elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of the TnsC-TnsD-att DNA complex and the TnsABCD transpososome from the Tn7-like transposon in Peltigera membranacea cyanobiont 210A, a type I-B CRISPR-associated transposon. Our structures reveal a striking bending of the att DNA, featured by the intercalation of an arginine side chain of TnsD into a CC/GG dinucleotide step. The TnsABCD transpososome structure reveals TnsA-TnsB interactions and demonstrates that TnsC not only recruits TnsAB but also directly participates in the transpososome assembly. These findings provide mechanistic insights into targeted DNA insertion by Tn7-like transposons, with implications for improving the precision and efficiency of their genome-editing applications.
History
DepositionNov 26, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42941.png

Downloads & links

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Map

FileDownload / File: emd_42941.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å		0.82 Å/pix.
x 360 pix.
= 295.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.034
Minimum - Maximum-0.0017732274 - 2.323038
Average (Standard dev.)0.002113918 (±0.034398966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 295.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_42941_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42941_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associ...

EntireName: Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associated transposon system
Components
  • Complex: Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associated transposon system
    • Protein or peptide: TnsC
    • DNA: DNA (41-MER)
    • DNA: DNA (41-MER)
    • Protein or peptide: TnsD
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associ...

SupramoleculeName: Ternary complex of TnsC, TnsD, and DNA in type I-B2 CRISPR-associated transposon system
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Peltigera membranacea (fungus)

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Macromolecule #1: TnsC

MacromoleculeName: TnsC / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Peltigera membranacea (fungus)
Molecular weightTheoretical: 43.521934 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKSTGFPLE LLTRPATERL AYFENYTVAH PRLKEVYEIL MRTIAEPAGA SFIFVYGASG VGKTTLRLRV EQKLTELALP KLESDRARV PVVGIEAIAP ESRYFNWKEY YTRALITLEE PLIDHKFDYG VRGISRDNFG KINVESKVVA PALRRALENA L IHRHPDVF ...String:
MTKSTGFPLE LLTRPATERL AYFENYTVAH PRLKEVYEIL MRTIAEPAGA SFIFVYGASG VGKTTLRLRV EQKLTELALP KLESDRARV PVVGIEAIAP ESRYFNWKEY YTRALITLEE PLIDHKFDYG VRGISRDNFG KINVESKVVA PALRRALENA L IHRHPDVF FVDEAQHFGK VASGYKLQDQ LDCLKSLANM TGILHCLLGT YELLTFRNLS GQLSRRSVDI HFRRYCADSP ED VQAFKSV LLTFQQHLPL AETPNLVDHW EYFYERTLGC IGTLKDWLKR VLSDALDREA TTITLKDLQK RALSVAQCQK MFK EIQEGE RQLSETEADV QNLRSALGLG AKPIVLPEET PKTTRPPGKV GKRKPKRDPI GVQQDVS

UniProtKB: ORC1/DEAH AAA+ ATPase domain-containing protein

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Macromolecule #4: TnsD

MacromoleculeName: TnsD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Peltigera membranacea (fungus)
Molecular weightTheoretical: 52.821109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MLASVLETYE SWNLKKPLIP QRSRLYQPQP VGIGTPYIES LTGYITRIAE LHGVLPGVLM TREIAPLVNK IYFQNGANRG FREIFNRSQ ALNGMGEMAA DLVQVLQKLT LRDDLRFLTM LFWSNILTPR NLFRTRKAWC PICYQERHQN GLVVYEQLLW T INLITICP ...String:
MLASVLETYE SWNLKKPLIP QRSRLYQPQP VGIGTPYIES LTGYITRIAE LHGVLPGVLM TREIAPLVNK IYFQNGANRG FREIFNRSQ ALNGMGEMAA DLVQVLQKLT LRDDLRFLTM LFWSNILTPR NLFRTRKAWC PICYQERHQN GLVVYEQLLW T INLITICP QHQKPLVELC PHCNHESPLL NWRSRPGYCS KCGEWLGANQ CLKTFTDGEG SIKLQLEWQY WTANVVGELI LA SQCFESA PSKENITKSL NIVIDKVAEN NAAAFSRLIG VPKNSLWMWQ STKTLPELNT LLKICYELEI SLVEFLTPKN LIT KSFTKI SQKHLQLSRT PRVSPKSFDQ YQVKDALLAI LAGNEEPPPT MEEVGKRLGH HNRTISRHFP DLCSAISAKC RNYN KACRL KSIEKLCSEV REIVLSLNAQ GVYPTEGRVC ELMPNPGCFR YKQVRAAFND ARREFGL

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Macromolecule #2: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Peltigera membranacea (fungus)
Molecular weightTheoretical: 24.727807 KDa
SequenceString: (DG)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DC) (DA)(DT)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DC) (DT)(DG)(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DG) (DT) (DG)(DA)(DT)(DC)(DT)(DT) ...String:
(DG)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DC) (DA)(DT)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DT)(DA)(DC) (DT)(DG)(DC)(DC)(DC)(DA)(DG)(DT)(DA)(DG) (DT) (DG)(DA)(DT)(DC)(DT)(DT)(DA)(DT) (DT)(DT)(DC)(DA)(DT)(DT)(DA)(DT)(DG)(DG) (DT)(DG) (DA)(DA)(DA)(DG)(DT)(DT)(DG) (DG)(DA)(DA)(DC)(DC)(DT)(DC)(DT)(DT)(DA) (DC)(DG)(DT)

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Macromolecule #3: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Peltigera membranacea (fungus)
Molecular weightTheoretical: 24.608814 KDa
SequenceString: (DA)(DC)(DG)(DT)(DA)(DA)(DG)(DA)(DG)(DG) (DT)(DT)(DC)(DC)(DA)(DA)(DC)(DT)(DT)(DT) (DC)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DT) (DG)(DA)(DA)(DA)(DT)(DA)(DA)(DG)(DA)(DT) (DC) (DA)(DC)(DT)(DA)(DC)(DT) ...String:
(DA)(DC)(DG)(DT)(DA)(DA)(DG)(DA)(DG)(DG) (DT)(DT)(DC)(DC)(DA)(DA)(DC)(DT)(DT)(DT) (DC)(DA)(DC)(DC)(DA)(DT)(DA)(DA)(DT) (DG)(DA)(DA)(DA)(DT)(DA)(DA)(DG)(DA)(DT) (DC) (DA)(DC)(DT)(DA)(DC)(DT)(DG)(DG) (DG)(DC)(DA)(DG)(DT)(DA)(DC)(DC)(DA)(DG) (DA)(DC) (DT)(DC)(DG)(DA)(DA)(DC)(DT) (DG)(DA)(DT)(DG)(DA)(DC)(DA)(DT)(DC)(DC) (DT)(DG)(DC)

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 7 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 7 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154947
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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