[English] 日本語
Yorodumi
- EMDB-42497: Spo11 core complex with gapped DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42497
TitleSpo11 core complex with gapped DNA
Map data
Sample
  • Complex: Spo11 core complex bound to gapped DNA
    • Protein or peptide: Meiotic recombination protein REC104
    • Protein or peptide: Meiotic recombination protein REC102
    • Protein or peptide: Meiosis-specific protein SPO11
    • Protein or peptide: Antiviral protein SKI8
    • DNA: gapped DNA
  • Ligand: MAGNESIUM ION
KeywordsSpo11 / Rec102 / Rec104 / Ski8 / DNA binding / Cross over. / DNA BINDING PROTEIN
Function / homology
Function and homology information


meiotic DNA double-strand break processing / mRNA decay by 3' to 5' exoribonuclease / meiotic DNA double-strand break formation / protein-DNA complex assembly / Ski complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / DNA end binding / synaptonemal complex assembly / homologous chromosome pairing at meiosis ...meiotic DNA double-strand break processing / mRNA decay by 3' to 5' exoribonuclease / meiotic DNA double-strand break formation / protein-DNA complex assembly / Ski complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / DNA end binding / synaptonemal complex assembly / homologous chromosome pairing at meiosis / meiosis I / 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 / nuclear-transcribed mRNA catabolic process / condensed nuclear chromosome / site of double-strand break / 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 / REC102 protein / 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 / Topoisomerase 6 subunit A/Spo11, Toprim domain ...Meiotic recombination protein Rec104 / : / Meiotic recombination protein REC104 / REC102 protein / 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 / Topoisomerase 6 subunit A/Spo11, Toprim domain / Topoisomerase (Topo) IIB-type catalytic domain profile. / : / 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
Meiosis-specific protein SPO11 / Meiotic recombination protein REC104 / Meiotic recombination protein REC102 / Antiviral protein SKI8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYu Y / Patel DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 HD110120 United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cryo-EM structures of the Spo11 core complex bound to DNA.
Authors: You Yu / Juncheng Wang / Kaixian Liu / Zhi Zheng / Meret Arter / Corentin Claeys Bouuaert / Stephen Pu / Dinshaw J Patel / Scott Keeney /
Abstract: DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data ...DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data have not been available, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-electron microscopy structures at up to 3.3-Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104 and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3'-OH and first 5' overhanging nucleotide, establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.
History
DepositionOct 26, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42497.png

Downloads & links

-
Map

FileDownload / File: emd_42497.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å		1.06 Å/pix.
x 256 pix.
= 272.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-3.7855744 - 4.7713423
Average (Standard dev.)0.00094772293 (±0.082780994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_42497_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_42497_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Spo11 core complex bound to gapped DNA

EntireName: Spo11 core complex bound to gapped DNA
Components
  • Complex: Spo11 core complex bound to gapped DNA
    • Protein or peptide: Meiotic recombination protein REC104
    • Protein or peptide: Meiotic recombination protein REC102
    • Protein or peptide: Meiosis-specific protein SPO11
    • Protein or peptide: Antiviral protein SKI8
    • DNA: gapped DNA
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Spo11 core complex bound to gapped DNA

SupramoleculeName: Spo11 core complex bound to gapped DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 140 KDa

-
Macromolecule #1: Meiotic recombination protein REC104

MacromoleculeName: Meiotic recombination protein REC104 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 20.763146 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
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

MacromoleculeName: Meiotic recombination protein REC102 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 30.263717 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

MacromoleculeName: Meiosis-specific protein SPO11 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 50.020109 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

MacromoleculeName: Antiviral protein SKI8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 44.313555 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

MacromoleculeName: gapped DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 21.943064 KDa
SequenceString: (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

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
Details: 25 mM HEPES, pH 7.4, 300 mM NaCl, 5 mM EDTA, 2 mM DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 548674
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more