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- EMDB-61291: Cryo-EM structure of Tdk1 tetramer complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61291
TitleCryo-EM structure of Tdk1 tetramer complex
Map data
Sample
  • Complex: Tdk1 tetramer
    • Protein or peptide: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
Keywordssignaling protein / meiotic cell cycle / CELL CYCLE
Function / homology
Function and homology information


meiotic drive / IgG binding / meiotic cell cycle / extracellular region / nucleoplasm
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsZhang J / Ye K
Funding support China, 3 items
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, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61291.png

Downloads & links

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Map

FileDownload / File: emd_61291.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 320 pix.
= 256. Å		0.8 Å/pix.
x 320 pix.
= 256. Å		0.8 Å/pix.
x 320 pix.
= 256. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.0017816115 - 1.9736061
Average (Standard dev.)0.0009884859 (±0.02562352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61291_msk_1.map
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Half map: #2

Fileemd_61291_half_map_1.map
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Histogram

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Half map: #1

Fileemd_61291_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tdk1 tetramer

EntireName: Tdk1 tetramer
Components
  • Complex: Tdk1 tetramer
    • Protein or peptide: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G

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Supramolecule #1: Tdk1 tetramer

SupramoleculeName: Tdk1 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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).
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Meiotically up-regulated gene 135 protein,Immunoglobulin G-bindin...

MacromoleculeName: Meiotically up-regulated gene 135 protein,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. group G (bacteria)
Molecular weightTheoretical: 38.43668 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe 972h- (yeast)
SequenceString: MSEEDNRLNE LFANDLGVQP PCERSLKEGR RFLNDFEIAA KKKLLELERK ALEDKEKNLN FVVESERTLF NSKKRAFDND ECYNDRCKL FRGIVNEWGR SERTLDSLDE PPAWFRREMG EWKKAREEDK EWRKSTDERL ENLLNIVREI LDVQRDMRND L SNLTRKVD ...String:
MSEEDNRLNE LFANDLGVQP PCERSLKEGR RFLNDFEIAA KKKLLELERK ALEDKEKNLN FVVESERTLF NSKKRAFDND ECYNDRCKL FRGIVNEWGR SERTLDSLDE PPAWFRREMG EWKKAREEDK EWRKSTDERL ENLLNIVREI LDVQRDMRND L SNLTRKVD RMDMRLSRNN NMIMRSFRQP ITEVPFFNGD IPDPNLPRIT RIEDIDSLSE ENCTRYLKGY GVSYDENDQS LW KRQLAKA VGLTAAYDAS YTFSPFSSSE SGGGSSGGGS TYKLILNGKT LKGETTTEAV DAATAEKVFK QYANDNGVDG EWT YDDATK TFTVTE

UniProtKB: Meiotically up-regulated gene 135 protein, Meiotically up-regulated gene 135 protein, Immunoglobulin G-binding protein G

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
2.0 mMKH2PO4Potassium phosphate monobasic
4.0 mMNa2HPO4Sodium Phosphate Dibasic
136.0 mMNaClSodium chloride
2.6 mMKClPotassium chloride
GridModel: Homemade / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Tridiem 4K / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 787 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: ab-initio reconstruction to generate the initial model
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 37724
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Correlation coefficient
Output model

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

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