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- EMDB-45394: Human TOP3B-TDRD3 core complex in DNA rejoining state with ssDNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45394
TitleHuman TOP3B-TDRD3 core complex in DNA rejoining state with ssDNA 5'-GACAGATATT-3
Map data
Sample
  • Complex: human TOP3B-TDRD3 core complex with DNA
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • Protein or peptide: Tudor domain-containing protein 3
    • DNA: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3')
    • DNA: DNA (5'-D(*AP*TP*T)-3')
  • Ligand: MANGANESE (II) ION
KeywordsTopoisomerase / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization ...DNA topoisomerase III-beta-TDRD3 complex / RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / condensed chromosome / methylated histone binding / chromosome segregation / chromatin organization / DNA recombination / transcription coactivator activity / DNA repair / chromatin binding / Golgi apparatus / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Tudor domain-containing protein 3, UBA domain / : / DNA topoisomerase 3-like, TOPRIM domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. ...Tudor domain-containing protein 3, UBA domain / : / DNA topoisomerase 3-like, TOPRIM domain / RecQ mediated genome instability protein 1, N-terminal / RecQ mediated genome instability protein, N-terminal OB-fold superfamily / RMI1, N-terminal OB-fold domain / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / Tudor domain / UBA-like domain / Tudor domain profile. / TOPRIM / Tudor domain / Tudor domain / Ubiquitin associated domain / Toprim domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Toprim domain profile. / TOPRIM domain / UBA-like superfamily
Similarity search - Domain/homology
DNA topoisomerase 3-beta-1 / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsYang X / Chen X / Yang W / Pommier Y
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into human topoisomerase 3β DNA and RNA catalysis and nucleic acid gate dynamics.
Authors: Xi Yang / Xuemin Chen / Wei Yang / Yves Pommier /
Abstract: Type IA topoisomerases (TopoIAs) are present in all living organisms. They resolve DNA/RNA catenanes, knots and supercoils by breaking and rejoining single-stranded DNA/RNA segments and allowing the ...Type IA topoisomerases (TopoIAs) are present in all living organisms. They resolve DNA/RNA catenanes, knots and supercoils by breaking and rejoining single-stranded DNA/RNA segments and allowing the passage of another nucleic acid segment through the break. Topoisomerase III-β (TOP3B), the only RNA topoisomerase in metazoans, promotes R-loop disassembly and translation of mRNAs. Defects in TOP3B lead to severe neurological diseases. We present a series of cryo-EM structures of human TOP3B with its cofactor TDRD3 during cleavage and rejoining of DNA or RNA, thus elucidating the roles of divalent metal ions and key enzyme residues in each step of the catalytic cycle. We also obtained the structure of an open-gate configuration that addresses the long-standing question of the strand-passage mechanism. Our studies reveal how TOP3B catalyzes both DNA and RNA relaxation, while TOP3A acts only on DNA.
History
DepositionJun 17, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45394.png

Downloads & links

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Map

FileDownload / File: emd_45394.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å		0.83 Å/pix.
x 352 pix.
= 292.16 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.03611925 - 1.9712858
Average (Standard dev.)0.0007468376 (±0.019828891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 292.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45394_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: #2

Fileemd_45394_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : human TOP3B-TDRD3 core complex with DNA

EntireName: human TOP3B-TDRD3 core complex with DNA
Components
  • Complex: human TOP3B-TDRD3 core complex with DNA
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • Protein or peptide: Tudor domain-containing protein 3
    • DNA: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3')
    • DNA: DNA (5'-D(*AP*TP*T)-3')
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: human TOP3B-TDRD3 core complex with DNA

SupramoleculeName: human TOP3B-TDRD3 core complex with DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA topoisomerase 3-beta-1

MacromoleculeName: DNA topoisomerase 3-beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA topoisomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.119867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VMKTVLMVAE MPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL ...String:
VMKTVLMVAE MPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL GEPDHNEALS VDARQELDLR IGCAFTRFQT KYFQGKYGDL DSSLISFGPC QTPTLGFCVE RHDKIQSFKP ET YWVLQAK VNTDKDRSLL LDWDRVRVFD REIAQMFLNM TKLEKEAQVE ATSRKEKAKQ RPLALNTVEM LRVASSSLGM GPQ HAMQTA ERLYTQGYIS (PTR)PRTETTHYP ENFDLKGSLR QQANHPYWAD TVKRLLAEGI NRPRKGHDAG DHPPITPMKS ATEAELGGD AWRLYEYITR HFIATVSHDC KYLQSTISFR IGPELFTCSG KTVLSPGFTE VMPWQSVPLE ESLPTCQRGD A FPVGEVKM LEKQTNPPDY LTEAELITLM EKHGIGTDAS IPVHINNICQ RNYVTVESGR RLKPTNLGIV LVHGYYKIDA EL VLPTIRS AVEKQLNLIA QGKADYRQVL GHTLDVFKRK FHYFVDSIAG MDELMEVSF

UniProtKB: DNA topoisomerase 3-beta-1

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Macromolecule #2: Tudor domain-containing protein 3

MacromoleculeName: Tudor domain-containing protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.428951 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAQVAGAALS QAGWYLSDEG IEACTSSPDK VNVNDIILIA LNTDLRTIGK KFLPSDINSG KVEKLEGPCV LQIQKIRNVA APKDNEESQ AAPRMLRLQM TDGHISCTAV EFSYMSKISL NTPPGTKVKL SGIVDIKNGF LLLNDSNTTV LGGEVEHLIE K W

UniProtKB: Tudor domain-containing protein 3

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Macromolecule #3: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3')

MacromoleculeName: DNA (5'-D(P*GP*AP*CP*AP*GP*AP*T)-3') / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.146449 KDa
SequenceString:
(DG)(DA)(DC)(DA)(DG)(DA)(DT)

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Macromolecule #4: DNA (5'-D(*AP*TP*T)-3')

MacromoleculeName: DNA (5'-D(*AP*TP*T)-3') / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 876.635 Da
SequenceString:
(DA)(DT)(DT)

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Macromolecule #5: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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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: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 770197
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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