9JA6 | pdb_00009ja6

Cryo-EM structure of Tdk1 tetramer complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural duality enables a single protein to act as a toxin-antidote pair for meiotic drive.

Hua, Y.Zhang, J.Yang, M.Y.Ren, J.Y.Suo, F.Liang, L.Dong, M.Q.Ye, K.Du, L.L.

(2024) Proc Natl Acad Sci U S A 121: e2408618121-e2408618121

  • DOI: https://doi.org/10.1073/pnas.2408618121
  • Primary Citation of Related Structures:  
    9JA6

  • PubMed Abstract: 

    In sexual reproduction, selfish genetic elements known as killer meiotic drivers (KMDs) bias inheritance by eliminating gametes that do not carry them. The selective killing behavior of most KMDs can be explained by a toxin-antidote model, where a toxin harms all gametes while an antidote provides resistance to the toxin in carriers. This study investigates whether and how the KMD element tdk1 in the fission yeast Schizosaccharomyces pombe deploys this strategy. Intriguingly, tdk1 relies on a single protein product, Tdk1, for both killing and resistance. We show that Tdk1 exists in a nontoxic tetrameric form during vegetative growth and meiosis but transforms into a distinct toxic form in spores. This toxic form acquires the ability to interact with the histone reader Bdf1 and assembles into supramolecular foci that disrupt mitosis in noncarriers after spore germination. In contrast, Tdk1 synthesized during germination of carrier spores is nontoxic and acts as an antidote, dismantling the preformed toxic Tdk1 assemblies. Replacement of the N-terminal region of Tdk1 with a tetramer-forming peptide reveals its dual roles in imposing an autoinhibited tetrameric conformation and facilitating the assembly of supramolecular foci when autoinhibition is released. Moreover, we successfully reconstituted a functional KMD element by combining a construct that exclusively expresses Tdk1 during meiosis ("toxin-only") with another construct that expresses Tdk1 specifically during germination ("antidote-only"). This work uncovers a remarkable example of a single protein employing structural duality to form a toxin-antidote pair, expanding our understanding of the mechanisms underlying toxin-antidote systems.


  • 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,Immunoglobulin G-binding protein G
A, B, C, D
332Schizosaccharomyces pombe 972h-Streptococcus sp. 'group GMutation(s): 0 
Gene Names: mug135SPCC330.04cspg
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP06654O74876
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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