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- PDB-8urq: Spo11 core complex with gapped DNA -

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Basic information

Entry
Database: PDB / ID: 8urq
TitleSpo11 core complex with gapped DNA
Components
  • (Meiotic recombination protein ...) x 2
  • Antiviral protein SKI8
  • Meiosis-specific protein SPO11
  • gapped DNA
KeywordsDNA BINDING PROTEIN / Spo11 / Rec102 / Rec104 / Ski8 / DNA binding / Cross over.
Function / homology
Function and homology information


meiotic DNA double-strand break processing / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / meiotic DNA double-strand break formation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, non-stop decay / : / DNA end binding ...meiotic DNA double-strand break processing / Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / meiotic DNA double-strand break formation / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, non-stop decay / : / DNA end binding / synaptonemal complex assembly / homologous chromosome pairing at meiosis / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / nuclear chromosome / sporulation resulting in formation of a cellular spore / mRNA catabolic process / condensed nuclear chromosome / protein-containing complex assembly / defense response to virus / chromatin binding / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
Meiotic recombination protein Rec104 / : / Meiotic recombination protein REC104 / Topoisomerase 6 subunit A/Spo11, Toprim domain / REC102 protein / Topoisomerase (Topo) IIB-type catalytic domain profile. / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily ...Meiotic recombination protein Rec104 / : / Meiotic recombination protein REC104 / Topoisomerase 6 subunit A/Spo11, Toprim domain / REC102 protein / Topoisomerase (Topo) IIB-type catalytic domain profile. / Spo11/DNA topoisomerase VI subunit A / Spo11/DNA topoisomerase VI, subunit A, N-terminal / Topoisomerase 6 subunit A/Spo11, TOPRIM domain / Spo11/DNA topoisomerase VI subunit A superfamily / Type IIB DNA topoisomerase / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Meiosis-specific protein SPO11 / Meiotic recombination protein REC104 / Meiotic recombination protein REC102 / Antiviral protein SKI8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu, Y. / Patel, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 HD110120 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the yeast Spo11 core complex bound to DNA
Authors: Yu, Y. / Wang, J.C. / Liu, K.X. / Zheng, Z. / Patel, D.J. / Keeney, S.
History
DepositionOct 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Meiotic recombination protein REC104
B: Meiotic recombination protein REC102
A: Meiosis-specific protein SPO11
C: Antiviral protein SKI8
D: gapped DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,3286
Polymers167,3045
Non-polymers241
Water00
1


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

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Components

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Meiotic recombination protein ... , 2 types, 2 molecules FB

#1: Protein Meiotic recombination protein REC104


Mass: 20763.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: REC104, YHR157W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33323
#2: Protein Meiotic recombination protein REC102


Mass: 30263.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: REC102, YLR329W, L8543.17 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02721

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Protein , 2 types, 2 molecules AC

#3: Protein Meiosis-specific protein SPO11


Mass: 50020.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SPO11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23179
#4: Protein Antiviral protein SKI8


Mass: 44313.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: SKI8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02793

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DNA chain / Non-polymers , 2 types, 2 molecules D

#5: DNA chain gapped DNA


Mass: 21943.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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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: Spo11 core complex bound to gapped DNA / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightValue: 0.14 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
Details: 25 mM HEPES, pH 7.4, 300 mM NaCl, 5 mM EDTA, 2 mM DTT
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 3 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: SerialEM / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 548674 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058855
ELECTRON MICROSCOPYf_angle_d0.70812089
ELECTRON MICROSCOPYf_dihedral_angle_d17.2851347
ELECTRON MICROSCOPYf_chiral_restr0.0441378
ELECTRON MICROSCOPYf_plane_restr0.0061410

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