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- EMDB-61290: Cryo-EM structure of Tdk1-Bdf1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-61290
TitleCryo-EM structure of Tdk1-Bdf1 complex
Map data
Sample
  • Complex: Tdk1-Bdf1 complex
    • Protein or peptide: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
  • Ligand: water
Keywordssignaling protein / meiotic cell cycle / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 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: 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, 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_61290.png

Downloads & links

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Map

FileDownload / File: emd_61290.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 307.2 Å		0.8 Å/pix.
x 384 pix.
= 307.2 Å		0.8 Å/pix.
x 384 pix.
= 307.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 10.0
Minimum - Maximum-63.759810000000002 - 119.526039999999995
Average (Standard dev.)0.02202644 (±1.7645885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61290_msk_1.map
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Additional map: #1

Fileemd_61290_additional_1.map
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Half map: #1

Fileemd_61290_half_map_1.map
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Half map: #2

Fileemd_61290_half_map_2.map
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Sample components

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Entire : Tdk1-Bdf1 complex

EntireName: Tdk1-Bdf1 complex
Components
  • Complex: Tdk1-Bdf1 complex
    • Protein or peptide: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
  • Ligand: water

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Supramolecule #1: Tdk1-Bdf1 complex

SupramoleculeName: Tdk1-Bdf1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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).
Source (natural)Organism: Schizosaccharomyces pombe 972h- (yeast)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomai...

MacromoleculeName: Meiotically up-regulated gene 135 protein,SWR1 complex bromodomain subunit bdf1,Immunoglobulin G-binding protein G
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. group G (bacteria)
Molecular weightTheoretical: 49.340484 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe 972h- (yeast)
SequenceString: MDEWRKSTDE WRKSTDERLE NLLNIVREIL DVQRDMRNDL SNLTRKVDRM DMRLSRNNNM IMRSFAQPIT EVPFFNGDIP DPNLPRITR IEDIDSLSEE NCTRYLKGYG VSYDENDQSL WKRQLAKAVG LTAAYDESYT FSPFSSSESG GGSGGGSGGG S GFKKASSS ...String:
MDEWRKSTDE WRKSTDERLE NLLNIVREIL DVQRDMRNDL SNLTRKVDRM DMRLSRNNNM IMRSFAQPIT EVPFFNGDIP DPNLPRITR IEDIDSLSEE NCTRYLKGYG VSYDENDQSL WKRQLAKAVG LTAAYDESYT FSPFSSSESG GGSGGGSGGG S GFKKASSS DNKEQGGGSG GGSGSGGGSQ EAETDALFDN GEEEEALMSE EEINGAKFAA VDKQISMLQD TLEAMKAKKM NR MRKPRRR DLTKEYGPIT YAMQNELAER CNYLSAEQLS NVAEILREEM PWLRDTDEIE IDVGNMKPEV FHRIYRYVCK PDA DSSEPA SPVLMPTKPE KKKGRVLSET EQAEKIRRLQ QQLDRFAGKT SPTSSGGGSS GGGSTYKLIL NGKTLKGETT TEAV DAATA EKVFKQYAND NGVDGEWTYD DATKTFTVTE GSGLEVLFQ

UniProtKB: Meiotically up-regulated gene 135 protein, SWR1 complex bromodomain subunit bdf1, Immunoglobulin G-binding protein G

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 123 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 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
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: 948 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.0) / Number images used: 288083
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-9ja5:
Cryo-EM structure of Tdk1-Bdf1 complex

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