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- PDB-9ja5: Cryo-EM structure of Tdk1-Bdf1 complex -

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Basic information

Entry
Database: PDB / ID: 9ja5
TitleCryo-EM structure of Tdk1-Bdf1 complex
ComponentsMeiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
KeywordsCELL CYCLE / signaling protein / meiotic cell cycle
Function / homology
Function and homology information


Swr1 complex / IgG binding / DNA repair-dependent chromatin remodeling / transcription initiation-coupled chromatin remodeling / meiotic cell cycle / chromatin remodeling / regulation of DNA-templated transcription / chromatin / 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 / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Meiotically up-regulated gene 135 protein / Immunoglobulin G-binding protein G / SWR1 complex bromodomain subunit bdf1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe 972h- (yeast)
Streptococcus sp. group G (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 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: A meiotic driver hijacks an epigenetic reader to disrupt mitosis in noncarrier offspring.
Authors: Yu Hua / Jianxiu Zhang / Man-Yun Yang / Fan-Yi Zhang / Jing-Yi Ren / Xiao-Hui Lyu / Yan Ding / Fang Suo / Guang-Can Shao / Jun Li / Meng-Qiu Dong / Keqiong Ye / Li-Lin Du /
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. ...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 is a single-gene KMD. This gene, , kills nearly all progeny in a × cross. By analyzing polymorphisms of among natural strains, we identify a resistant haplotype, HT3. This haplotype lacks killing ability yet confers resistance to killing by the wild-type . Proximity labeling experiments reveal an interaction between Tdk1, the protein product of , 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 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.
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,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
B: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
C: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
D: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
E: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
F: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G


Theoretical massNumber of molelcules
Total (without water)296,0436
Polymers296,0436
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody
Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G / IgG-binding protein G


Mass: 49340.484 Da / Num. of mol.: 6
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, bdf1, brf1, SPCC1450.02, SPCC191.13, spg
Production host: Schizosaccharomyces pombe 972h- (yeast)
References: UniProt: O74876, UniProt: Q9Y7N0, UniProt: P06654
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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-Bdf1 complex / Type: COMPLEX
Details: The fusion protein comprises of the residues 211-357 of Tdk1,a linker sequence(SGGGSGGGSGGGSGFKKASSSDNKEQGGGSGGGSGSGGGS), residues 372-554 of Bdf1, a linker sequence of (SGGGSSGGGS) and ...Details: The fusion protein comprises of the residues 211-357 of Tdk1,a linker sequence(SGGGSGGGSGGGSGFKKASSSDNKEQGGGSGGGSGSGGGS), residues 372-554 of Bdf1, a linker sequence of (SGGGSSGGGS) and residues 228-282 of Immunoglobulin G-binding protein G(GB1).
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.3 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.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 948
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288083 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0148472
ELECTRON MICROSCOPYf_angle_d1.12511406
ELECTRON MICROSCOPYf_dihedral_angle_d19.4451134
ELECTRON MICROSCOPYf_chiral_restr0.0641224
ELECTRON MICROSCOPYf_plane_restr0.0051518

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