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- PDB-9ca0: Human TOP3B-TDRD3 core complex in DNA pre-cleavage state -

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Basic information

Entry
Database: PDB / ID: 9ca0
TitleHuman TOP3B-TDRD3 core complex in DNA pre-cleavage state
Components
  • DNA (5'-D(*AP*TP*T)-3')
  • DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3')
  • DNA topoisomerase 3-beta-1
  • Tudor domain-containing protein 3
KeywordsISOMERASE/DNA / Topoisomerase / DNA / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase III-beta-TDRD3 complex / 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 / transcription coactivator activity ...DNA topoisomerase III-beta-TDRD3 complex / 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 / transcription coactivator activity / 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. / 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 / Tudor domain profile. / TOPRIM / UBA/TS-N domain / 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 topoisomerase 3-beta-1 / Tudor domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsYang, X. / Chen, X. / Yang, W. / Pommier, Y.
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: To Be Published
Title: Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics
Authors: Yang, X. / Chen, X. / Yang, W. / Pommier, Y.
History
DepositionJun 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: 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
D: DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3')
E: DNA (5'-D(*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5845
Polymers89,5294
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

#1: 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
#2: Protein Tudor domain-containing protein 3 / TDRD3


Mass: 17428.951 Da / Num. of mol.: 1 / 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
#3: DNA chain DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3')


Mass: 2105.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(*AP*TP*T)-3')


Mass: 876.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#5: 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
Has ligand of interestY

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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: human TOP3B-TDRD3 core complex with DNA / Type: COMPLEX / Entity ID: #1-#4 / 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54.4 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198867 / Symmetry type: POINT

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