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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Spo11 core complex with gapped DNA | |||||||||
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![]() | Spo11 / Rec102 / Rec104 / Ski8 / DNA binding / Cross over. / DNA BINDING PROTEIN | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Yu Y / Patel DJ | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the yeast Spo11 core complex bound to DNA Authors: Yu Y / Wang JC / Liu KX / Zheng Z / Patel DJ / Keeney S | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
Images | ![]() | 156.6 KB | ||
Filedesc metadata | ![]() | 6.8 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 774.5 KB | Display | ![]() |
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Full document | ![]() | 774.1 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 14.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8urqMC ![]() 8uruC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half Map A
File | emd_42497_half_map_1.map | ||||||||||||
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Annotation | Half Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half Map B
File | emd_42497_half_map_2.map | ||||||||||||
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Annotation | Half Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Spo11 core complex bound to gapped DNA
Entire | Name: Spo11 core complex bound to gapped DNA |
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Components |
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-Supramolecule #1: Spo11 core complex bound to gapped DNA
Supramolecule | Name: Spo11 core complex bound to gapped DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 140 KDa |
-Macromolecule #1: Meiotic recombination protein REC104
Macromolecule | Name: Meiotic recombination protein REC104 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 20.763146 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSIEEEDTNK ITCTQDFLHQ YFVTERVSIQ FGLNNKTVKR INKDEFDKAV NCIMSWTNYP KPGLKRTAST YLLSNSFKKS ATVSLPFIL GDPVCMPKRV ESNNNDTCLL YSDTLYDDPL IQRNDQAGDE IEDEFSFTLL RSEVNEIRPI SSSSTAQILQ S DYSALMYE RQASNGSIFQ FSSP UniProtKB: Meiotic recombination protein REC104 |
-Macromolecule #2: Meiotic recombination protein REC102
Macromolecule | Name: Meiotic recombination protein REC102 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 30.263717 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MARDITFLTV FLESCGAVNN DEAGKLLSAW TSTVRIEGPE STDSNSLYIP LLPPGMLKIK LNFKMNDRLV TEEQELFTKL REIVGSSIR FWEEQLFYQV QDVSTIENHV ILSLKCTILT DAQISTFISK PRELHTHAKG YPEIYYLSEL STTVNFFSKE G NYVEISQV ...String: MARDITFLTV FLESCGAVNN DEAGKLLSAW TSTVRIEGPE STDSNSLYIP LLPPGMLKIK LNFKMNDRLV TEEQELFTKL REIVGSSIR FWEEQLFYQV QDVSTIENHV ILSLKCTILT DAQISTFISK PRELHTHAKG YPEIYYLSEL STTVNFFSKE G NYVEISQV IPHFNEYFSS LIVSQLEFEY PMVFSMISRL RLKWQQSSLA PISYALTSNS VLLPIMLNMI AQDKSSTTAY QI LCRRRGP PIQNFQIFSL PAVTYNK UniProtKB: Meiotic recombination protein REC102 |
-Macromolecule #3: Meiosis-specific protein SPO11
Macromolecule | Name: Meiosis-specific protein SPO11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.020109 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MALEGLRKKY KTRQELVKAL TPKRRSIHLN SNGHSNGTPC SNADVLAHIK HFLSLAANSL EQHQQPISIV FQNKKKKGDT NSPDIHTTL DFPLNGPHLS THQFKLKRCA ILLNLLKVVM EKLPLGKNTT VRDIFYSNVE LFQRQANVVQ WLDVIRFNFK L SPRKSLNI ...String: MALEGLRKKY KTRQELVKAL TPKRRSIHLN SNGHSNGTPC SNADVLAHIK HFLSLAANSL EQHQQPISIV FQNKKKKGDT NSPDIHTTL DFPLNGPHLS THQFKLKRCA ILLNLLKVVM EKLPLGKNTT VRDIFYSNVE LFQRQANVVQ WLDVIRFNFK L SPRKSLNI IPAQKGLVYS PFPIDIYDNI LTCENEPKMQ KQTIFSGKPC LIPFFQDDAV IKLGTTSMCN IVIVEKEAVF TK LVNNYHK LSTNTMLITG KGFPDFLTRL FLKKLEQYCS NLISDCSIFT DADPYGISIA LNYTHSNERN AYICTMANYK GIR ITQVLA QNNEVHNKSI QLLSLNQRDY SLAKNLIASL TANSWDIATS PLKNVVIECQ REIFFQKKAE MNEIDAGIFK YKSR HHHHH HHHHHGDYKD DDDKDYKDDD DKDYKDDDDK UniProtKB: Meiosis-specific protein SPO11 |
-Macromolecule #4: Antiviral protein SKI8
Macromolecule | Name: Antiviral protein SKI8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 44.313555 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSKVFIATAN AGKAHDADIF SVSACNSFTV SCSGDGYLKV WDNKLLDNEN PKDKSYSHFV HKSGLHHVDV LQTIERDAFE LCLVATTSF SGDLLFYRIT REDETKKVIF EKLDLLDSDM KKHSFWALKW GASNDRLLSH RLVATDVKGT TYIWKFHPFA D ESNSLTLN ...String: MSKVFIATAN AGKAHDADIF SVSACNSFTV SCSGDGYLKV WDNKLLDNEN PKDKSYSHFV HKSGLHHVDV LQTIERDAFE LCLVATTSF SGDLLFYRIT REDETKKVIF EKLDLLDSDM KKHSFWALKW GASNDRLLSH RLVATDVKGT TYIWKFHPFA D ESNSLTLN WSPTLELQGT VESPMTPSQF ATSVDISERG LIATGFNNGT VQISELSTLR PLYNFESQHS MINNSNSIRS VK FSPQGSL LAIAHDSNSF GCITLYETEF GERIGSLSVP THSSQASLGE FAHSSWVMSL SFNDSGETLC SAGWDGKLRF WDV KTKERI TTLNMHCDDI EIEEDILAVD EHGDSLAEPG VFDVKFLKKG WRSGMGADLN ESLCCVCLDR SIRWFREAGG K UniProtKB: Antiviral protein SKI8 |
-Macromolecule #5: gapped DNA
Macromolecule | Name: gapped DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.943064 KDa |
Sequence | String: (DT)(DA)(DG)(DG)(DC)(DC)(DG)(DT)(DC)(DG) (DG)(DC)(DT)(DA)(DC)(DT)(DA)(DA)(DA)(DA) (DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DC) (DG)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DT)(DA) (DG) (DC)(DA)(DA)(DT)(DG)(DT) ...String: (DT)(DA)(DG)(DG)(DC)(DC)(DG)(DT)(DC)(DG) (DG)(DC)(DT)(DA)(DC)(DT)(DA)(DA)(DA)(DA) (DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DC) (DG)(DG)(DC)(DC)(DG)(DG)(DA)(DT)(DT)(DA) (DG) (DC)(DA)(DA)(DT)(DG)(DT)(DA)(DA) (DT)(DC)(DG)(DT)(DC)(DT)(DT)(DA)(DA)(DG) (DA)(DC) (DG)(DA)(DT)(DT)(DA)(DC)(DA) (DT)(DT)(DG)(DC) |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 Details: 25 mM HEPES, pH 7.4, 300 mM NaCl, 5 mM EDTA, 2 mM DTT |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 548674 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |