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- PDB-9ja6: Cryo-EM structure of Tdk1 tetramer complex -

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Basic information

Entry
Database: PDB / ID: 9ja6
TitleCryo-EM structure of Tdk1 tetramer complex
ComponentsMeiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
KeywordsCELL CYCLE / signaling protein / meiotic cell cycle
Function / homology
Function and homology information


IgG binding / meiotic cell cycle / extracellular region / nucleus
Similarity search - Function
Domain of unknown function DUF1773 / Mug135-like, C-terminal domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif ...Domain of unknown function DUF1773 / Mug135-like, C-terminal domain / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain
Similarity search - Domain/homology
Meiotically up-regulated gene 135 protein / Immunoglobulin G-binding protein G
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Streptococcus sp. group G (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhang, J. / Ye, K.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071199, 91940302 China
Chinese Academy of SciencesXDB37010201 China
National Basic Research Program of China (973 Program)2017YFA0504600 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural duality enables a single protein to act as a toxin-antidote pair for meiotic drive.
Authors: Yu Hua / Jianxiu Zhang / Man-Yun Yang / Jing-Yi Ren / Fang Suo / Lingfei Liang / Meng-Qiu Dong / Keqiong Ye / Li-Lin Du /
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 ...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 in the fission yeast deploys this strategy. Intriguingly, 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.
History
DepositionAug 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
B: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
C: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
D: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)153,7474
Polymers153,7474
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 38436.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe 972h- (yeast), (gene. exp.) Streptococcus sp. group G (bacteria)
Gene: mug135, SPCC330.04c, spg / Production host: Schizosaccharomyces pombe 972h- (yeast) / References: UniProt: O74876, UniProt: P06654
Has protein modificationN

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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: Tdk1 tetramer / Type: COMPLEX
Details: The fusion protein comprises of residues 1-129 and 220-357 of Tdk1, mutations A276R and E346A, a linker sequence(SGGGSSGGGS), and residues 228-282 of Immunoglobulin G-binding protein G(GB1).
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.15 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Schizosaccharomyces pombe 972h- (yeast)284812
21Streptococcus sp. group G (bacteria)1320
Source (recombinant)Organism: Schizosaccharomyces pombe 972h- (yeast)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
12 mMPotassium phosphate monobasicKH2PO41
24 mMSodium Phosphate DibasicNa2HPO41
3136 mMSodium chlorideNaCl1
42.6 mMPotassium chlorideKCl1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 5 seconds before plunging

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 787
EM imaging opticsEnergyfilter name: GIF Tridiem 4K / Energyfilter slit width: 20 eV
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.06CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARC3initial Euler assignment
11cryoSPARC3final Euler assignment
12cryoSPARC3classification
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37724 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0075332
ELECTRON MICROSCOPYf_angle_d0.8117188
ELECTRON MICROSCOPYf_dihedral_angle_d5.076708
ELECTRON MICROSCOPYf_chiral_restr0.043748
ELECTRON MICROSCOPYf_plane_restr0.004948

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