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- EMDB-45374: Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble -

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Basic information

Entry
Database: EMDB / ID: EMD-45374
TitleDimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Map data
Sample
  • Complex: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • Protein or peptide: Tudor domain-containing protein 3
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • DNA: DNA (5'-D(P*CP*AP*GP*AP*TP*CP*AP*GP*AP*AP*TP*GP*AP*AP*TP*AP*TP*AP*CP*TP*AP*AP*A)-3')
    • DNA: DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')
    • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION
KeywordsTopoisomerase / DNA / Supercoiling / 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 / : / 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 / : / 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
: / DNA topoisomerase 3-beta zinc ribbon domain / 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 3-beta zinc ribbon domain / 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: 4.25 Å
AuthorsYang X
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 16, 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_45374.png

Downloads & links

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Map

FileDownload / File: emd_45374.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0017683562 - 1.8685821
Average (Standard dev.)0.0017171769 (±0.030180981)
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_45374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45374_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble

EntireName: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble
Components
  • Complex: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • Protein or peptide: Tudor domain-containing protein 3
    • Protein or peptide: DNA topoisomerase 3-beta-1
    • DNA: DNA (5'-D(P*CP*AP*GP*AP*TP*CP*AP*GP*AP*AP*TP*GP*AP*AP*TP*AP*TP*AP*CP*TP*AP*AP*A)-3')
    • DNA: DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')
    • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble

SupramoleculeName: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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: 69.037875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VMKTVLMVAE KPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL ...String:
VMKTVLMVAE KPSLAQSIAK 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 YPRTETTHYP ENFDLKGSLR QQANHPYWAD TVKRLLAEGI NRPRKGHDAG DHPPITPMKS ATEA ELGGD AWRLYEYITR HFIATVSHDC KYLQSTISFR IGPELFTCSG KTVLSPGFTE VMPWQSVPLE ESLPTCQRGD AFPVG EVKM LEKQTNPPDY LTEAELITLM EKHGIGTDAS IPVHINNICQ RNYVTVESGR RLKPTNLGIV LVHGYYKIDA ELVLPT IRS 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: 2 / 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 topoisomerase 3-beta-1

MacromoleculeName: DNA topoisomerase 3-beta-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA topoisomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.117852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VMKTVLMVAE KPSLAQSIAK ILSRGSLSSH KGLNGACSVH EYTGTFAGQP VRFKMTSVCG HVMTLDFLGK YNKWDKVDPA ELFSQAPTE KKEANPKLNM VKFLQVEGRG CDYIVLWLDC DKEGENICFE VLDAVLPVMN KAHGGEKTVF RARFSSITDT D ICNAMACL ...String:
VMKTVLMVAE KPSLAQSIAK 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 #4: DNA (5'-D(P*CP*AP*GP*AP*TP*CP*AP*GP*AP*AP*TP*GP*AP*AP*TP*AP*TP*AP...

MacromoleculeName: DNA (5'-D(P*CP*AP*GP*AP*TP*CP*AP*GP*AP*AP*TP*GP*AP*AP*TP*AP*TP*AP*CP*TP*AP*AP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.089651 KDa
SequenceString:
(DC)(DA)(DG)(DA)(DT)(DC)(DA)(DG)(DA)(DA) (DT)(DG)(DA)(DA)(DT)(DA)(DT)(DA)(DC)(DT) (DA)(DA)(DA)

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Macromolecule #5: DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*...

MacromoleculeName: DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')
type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.890818 KDa
SequenceString:
(DA)(DT)(DT)(DG)(DG)(DA)(DG)(DT)(DT)(DC) (DA)(DT)(DG)(DT)(DG)(DA)(DT)(DG)(DC)

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Macromolecule #6: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.379841 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DA)(DT)(DG) (DA)(DA)(DC)(DT)(DC)(DC)(N)(N)(N)(N) (DG) (DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT) (DT)(DC)(DA)(DT)(DT)(DC)(DT)(DG)(DA)(DT) (DC)(DT) (DG)

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Macromolecule #7: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 1 / 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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 63358
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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