9CA1

Human TOP3B-TDRD3 core complex in DNA religation state

  • Classification: ISOMERASE/DNA
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2024-06-16 Released: 2024-07-17 
  • Deposition Author(s): Yang, X., Chen, X., Yang, W., Pommier, Y.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural Insights into human Topoisomerase 3-beta DNA and RNA catalytic cycles and topo-gate dynamics

Yang, X., Chen, X., Yang, W., Pommier, Y.

To be published.

Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 3-beta-1612Homo sapiensMutation(s): 1 
Gene Names: TOP3B, TOP3B1
EC: 5.6.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for O95985 (Homo sapiens)
Explore O95985 
Go to UniProtKB:  O95985
PHAROS:  O95985
GTEx:  ENSG00000100038 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95985
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tudor domain-containing protein 3161Homo sapiensMutation(s): 0 
Gene Names: TDRD3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7E2 (Homo sapiens)
Explore Q9H7E2 
Go to UniProtKB:  Q9H7E2
PHAROS:  Q9H7E2
GTEx:  ENSG00000083544 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7E2
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*TP*AP*CP*TP*AP*AP*A)-3')C [auth D]7Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*T)-3')D [auth E]3Homo sapiens
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
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--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary