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- PDB-9c9w: Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble -

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Basic information

Entry
Database: PDB / ID: 9c9w
TitleDimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Components
  • (DNA topoisomerase 3-beta- ...) x 2
  • DNA (38-MER)
  • DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')
  • 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')
  • Tudor domain-containing protein 3
KeywordsISOMERASE/DNA / Topoisomerase / 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 / DNA (> 10) / DNA topoisomerase 3-beta-1 / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsYang, X.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 3-beta-1
B: Tudor domain-containing protein 3
C: DNA topoisomerase 3-beta-1
D: Tudor domain-containing protein 3
E: 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')
F: DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')
L: DNA (38-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,4298
Polymers198,3747
Non-polymers551
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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DNA topoisomerase 3-beta- ... , 2 types, 2 molecules AC

#1: Protein DNA topoisomerase 3-beta-1 / DNA topoisomerase III beta-1


Mass: 69037.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP3B, TOP3B1 / Production host: Homo sapiens (human) / References: UniProt: O95985, DNA topoisomerase
#3: Protein DNA topoisomerase 3-beta-1 / DNA topoisomerase III beta-1


Mass: 69117.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOP3B, TOP3B1 / Production host: Homo sapiens (human) / References: UniProt: O95985, DNA topoisomerase

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DNA chain , 3 types, 3 molecules EFL

#4: DNA chain 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')


Mass: 7089.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: DNA chain DNA (5'-D(*AP*TP*TP*GP*GP*AP*GP*TP*TP*CP*AP*TP*GP*TP*GP*AP*TP*GP*C)-3')


Mass: 5890.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (38-MER)


Mass: 12379.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein / Non-polymers , 2 types, 3 molecules BD

#2: Protein Tudor domain-containing protein 3 / TDRD3


Mass: 17428.951 Da / Num. of mol.: 2 / Fragment: DUF-OB fold (UNP residues 1-161)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TDRD3 / Production host: Homo sapiens (human) / References: UniProt: Q9H7E2
#7: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimerized human TOP3B-TDRD3 core complexes with a DNA mismatch bubble
Type: COMPLEX / Entity ID: #1-#6 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63358 / Symmetry type: POINT

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