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- EMDB-37479: The cryo-EM structure of TdpAB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-37479
TitleThe cryo-EM structure of TdpAB complex
Map data
Sample
  • Complex: TdpAB complex
    • Protein or peptide: TdpB
    • Protein or peptide: TdpA
KeywordsDNA phosphorothioation / antiphage / translocase / nuclease
Biological speciesThermus antranikianii DSM 12462 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsAn T / Tan Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: A DNA phosphorothioation pathway via adenylated intermediate modulates Tdp machinery.
Authors: Tianchen An / Qian Tan / Lixu Jiang / Li Liu / Xing Jiang / Liying Liu / Xiaofei Chang / Xihao Tian / Zixin Deng / Shuai Gao / Lianrong Wang / Shi Chen /
Abstract: In prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism ...In prokaryotes, the non-bridging oxygen in the DNA sugar-phosphate backbone can be enzymatically replaced by a sulfur atom, resulting in phosphorothioate (PT) modification. However, the mechanism underlying the oxygen-to-sulfur substitution remains enigmatic. In this study, we discovered a hypercompact DNA phosphorothioation system, TdpABC, in extreme thermophiles. This DNA sulfuration process occurs through two sequential steps: an initial activation step by ATP to form an adenylated intermediate, followed by a substitution step where the adenyl group is replaced with a sulfur atom. Together with the TdpA-TdpB, the TdpABC system provides anti-phage defense by degrading PT-free phage DNA. Cryogenic electron microscopy structural analysis revealed that the TdpA hexamer binds one strand of encircled duplex DNA via hydrogen bonds arranged in a spiral staircase conformation. Nevertheless, the TdpAB-DNA interaction was sensitive to the hydrophobicity of the PT sulfur. PTs inhibit ATP-driven translocation and nuclease activity of TdpAB on self-DNA, thereby preventing autoimmunity.
History
DepositionSep 18, 2023-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37479.png

Downloads & links

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Map

FileDownload / File: emd_37479.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.48217207 - 0.7487981
Average (Standard dev.)0.0012931939 (±0.03222106)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37479_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_37479_half_map_2.map
Projections & Slices
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Sample components

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Entire : TdpAB complex

EntireName: TdpAB complex
Components
  • Complex: TdpAB complex
    • Protein or peptide: TdpB
    • Protein or peptide: TdpA

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Supramolecule #1: TdpAB complex

SupramoleculeName: TdpAB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermus antranikianii DSM 12462 (bacteria)

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Macromolecule #1: TdpB

MacromoleculeName: TdpB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermus antranikianii DSM 12462 (bacteria)
Molecular weightTheoretical: 42.757934 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPYAGEGSNP LGLKDFLDDL RLDHYQDLLR ELDELYQKLK QERQVPLHGD GEAYPLLTLT VDGGEGRAFE ELPLLSFGLV RVAAVGVKG FRLPSIAHLL PGYEVLRDPK GYLEGLLERS EESPAADALK TFFRATGISL EDLGEYYTKD LRAFMGIFRD V LEWAYLVW ...String:
MPYAGEGSNP LGLKDFLDDL RLDHYQDLLR ELDELYQKLK QERQVPLHGD GEAYPLLTLT VDGGEGRAFE ELPLLSFGLV RVAAVGVKG FRLPSIAHLL PGYEVLRDPK GYLEGLLERS EESPAADALK TFFRATGISL EDLGEYYTKD LRAFMGIFRD V LEWAYLVW GVEKVLQESY KDYLFIKDGR LAQLGVRESF RSKLQNYFAR KHLLLAGVTK RSRLLAEGLT SLVMARLFAE AR GTFVLQV PQELMEKAYR YERQWNADLE GAFVMGRRYV ARLLEDTFRP QEGVAIFDLP PYLGEEDAVK VARSLRAHRS VLY GGSVGT VVEAHGRASV ARSIPRRMEE EILARFRKAF GEDLAKKLTE WLRLADRED

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Macromolecule #2: TdpA

MacromoleculeName: TdpA / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Thermus antranikianii DSM 12462 (bacteria)
Molecular weightTheoretical: 66.546008 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAESPIGVVV SSRRNGPWAE LTLVLTPQEL DQGKRLLLGE LVRVSSGGKD YVGMVLDGYY EPVGRSDPTY TLALAHINQV DLEKEDPWA RKEVNFYHHR IVLLGRVVQG GLFAPSTRLL PPVVEARVYR MTEEELQRLL AAEVRTSGSV KAEGKRRYAF G HLAYGLEE ...String:
MAESPIGVVV SSRRNGPWAE LTLVLTPQEL DQGKRLLLGE LVRVSSGGKD YVGMVLDGYY EPVGRSDPTY TLALAHINQV DLEKEDPWA RKEVNFYHHR IVLLGRVVQG GLFAPSTRLL PPVVEARVYR MTEEELQRLL AAEVRTSGSV KAEGKRRYAF G HLAYGLEE GGEYPEVVKE VDPALFVGRR TANFGKTGFG KSNENKVILT LLAHAFPRVG MLILDQNAEY LLQTEATTSP GL AQAFKAL GIRGRIRFYT AREEAWARRL KEHLGTEWRE YVEVLPLKVD FYHFPELAVA LAYQRRRLQG AEPPQYLENA FYN LEDWKH IPDRMAYVYG ALRKAGLTPR KGLKIKYKNE NYDISEEKSW GNLQEAMENN SQRGDNKGGA RELYSRAKVF SFLR AFHAP GKEANFLETI KEDLLGEKTE GEGKVVILDL PSLGEAADFF TLRLMDLLFD RAVELYGKRQ ANFLVVLEEA HNFLE DKAG IFYRVAKEGR KYGIGMLYST QSPASIPMEI LSQTENFLVK HLSSEEDVKV LKRAKAPFAF VADFLLSEPI IGYSYV YFE PYQPFVVPLR VKLLEHVLKS LDS

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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: 8
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63488
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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