9JA5 | pdb_00009ja5

Cryo-EM structure of Tdk1-Bdf1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

A meiotic driver hijacks an epigenetic reader to disrupt mitosis in noncarrier offspring.

Hua, Y.Zhang, J.Yang, M.Y.Zhang, F.Y.Ren, J.Y.Lyu, X.H.Ding, Y.Suo, F.Shao, G.C.Li, J.Dong, M.Q.Ye, K.Du, L.L.

(2024) Proc Natl Acad Sci U S A 121: e2408347121-e2408347121

  • DOI: https://doi.org/10.1073/pnas.2408347121
  • Primary Citation of Related Structures:  
    9JA5

  • PubMed Abstract: 

    Killer meiotic drivers (KMDs) are selfish genetic elements that distort Mendelian inheritance by selectively killing meiotic products lacking the KMD element, thereby promoting their own propagation. Although KMDs have been found in diverse eukaryotes, only a limited number of them have been characterized at the molecular level, and their killing mechanisms remain largely unknown. In this study, we identify that a gene previously deemed essential for cell survival in the fission yeast Schizosaccharomyces pombe is a single-gene KMD. This gene, tdk1 , kills nearly all tdk1Δ progeny in a tdk1+ × tdk1Δ cross. By analyzing polymorphisms of tdk1 among natural strains, we identify a resistant haplotype, HT3. This haplotype lacks killing ability yet confers resistance to killing by the wild-type tdk1 . Proximity labeling experiments reveal an interaction between Tdk1, the protein product of tdk1 , and the epigenetic reader Bdf1. Interestingly, the nonkilling Tdk1-HT3 variant does not interact with Bdf1. Cryoelectron microscopy further elucidated the binding interface between Tdk1 and Bdf1, pinpointing mutations within Tdk1-HT3 that disrupt this interface. During sexual reproduction, Tdk1 forms stable Bdf1-binding nuclear foci in all spores after meiosis. These foci persist in germinated tdk1Δ progeny and impede chromosome segregation during mitosis by generating aberrant chromosomal adhesions. This study identifies a KMD that masquerades as an essential gene and reveals the molecular mechanism by which this KMD hijacks cellular machinery to execute killing. Additionally, we unveil that losing the hijacking ability is an evolutionary path for this single-gene KMD to evolve into a nonkilling resistant haplotype.


  • Organizational Affiliation
    • National Institute of Biological Sciences, Beijing 102206, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
A, B, C, D, E
A, B, C, D, E, F
444Schizosaccharomyces pombe 972h-Streptococcus sp. 'group GMutation(s): 0 
Gene Names: mug135SPCC330.04cbdf1brf1SPCC1450.02SPCC191.13spg
UniProt
Find proteins for O74876 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O74876 
Go to UniProtKB:  O74876
Find proteins for P06654 (Streptococcus sp. group G)
Explore P06654 
Go to UniProtKB:  P06654
Find proteins for Q9Y7N0 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q9Y7N0 
Go to UniProtKB:  Q9Y7N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP06654Q9Y7N0O74876
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32071199, 91940302
Chinese Academy of SciencesChinaXDB37010201
National Basic Research Program of China (973 Program)China2017YFA0504600

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-13
    Type: Initial release