+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27030 | |||||||||
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Title | Structure of S. cerevisiae Hop1 CBR bound to a nucleosome | |||||||||
Map data | Nucleosome CBR | |||||||||
Sample |
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Keywords | meiosis / recombination / chromosome axis / nucleosome / PHD / winged helix / DNA BINDING PROTEIN-DNA complex | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.74 Å | |||||||||
Authors | Gu Y / Ur SN / Milano CR / Tromer EC / Vale-Silva LA / Hochwagen A / Corbett KD | |||||||||
Funding support | United States, 1 items
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Citation | Journal: EMBO J / Year: 2024 Title: Chromatin binding by HORMAD proteins regulates meiotic recombination initiation. Authors: Carolyn R Milano / Sarah N Ur / Yajie Gu / Jessie Zhang / Rachal Allison / George Brown / Matthew J Neale / Eelco C Tromer / Kevin D Corbett / Andreas Hochwagen / Abstract: The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates ...The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27030.map.gz | 32.4 MB | EMDB map data format | |
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Header (meta data) | emd-27030-v30.xml emd-27030.xml | 25 KB 25 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27030_fsc.xml | 8.8 KB | Display | FSC data file |
Images | emd_27030.png | 166.2 KB | ||
Filedesc metadata | emd-27030.cif.gz | 6.8 KB | ||
Others | emd_27030_additional_1.map.gz emd_27030_half_map_1.map.gz emd_27030_half_map_2.map.gz | 32.2 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27030 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27030 | HTTPS FTP |
-Validation report
Summary document | emd_27030_validation.pdf.gz | 1003.4 KB | Display | EMDB validaton report |
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Full document | emd_27030_full_validation.pdf.gz | 1003 KB | Display | |
Data in XML | emd_27030_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | emd_27030_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27030 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27030 | HTTPS FTP |
-Related structure data
Related structure data | 8cwwMC 7ubaC 8czeC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27030.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Nucleosome CBR | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: local map for CBR
File | emd_27030_additional_1.map | ||||||||||||
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Annotation | local map for CBR | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27030_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27030_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Hop1 CBR domain bound to nucleosome
Entire | Name: Complex of Hop1 CBR domain bound to nucleosome |
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Components |
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-Supramolecule #1: Complex of Hop1 CBR domain bound to nucleosome
Supramolecule | Name: Complex of Hop1 CBR domain bound to nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 223 KDa |
-Macromolecule #1: Meiosis-specific protein HOP1
Macromolecule | Name: Meiosis-specific protein HOP1 / type: protein_or_peptide / ID: 1 / Details: GenBank:DAA08478.1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 24.239928 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SNASNNPVTG ICSCECGLEV PKAATVLKTC KSCRKTLHGI CYGNFLHSSI EKCFTCIFGP SLDTKWSKFQ DLMMIRKVFR FLVRKKKGF PASITELIDS FINVEDQNNE VKERVAFALF VFFLDETLCL DNGGKPSQTI RYVTSSVLVD VKGIVIPNTR K QLNVNHEY ...String: SNASNNPVTG ICSCECGLEV PKAATVLKTC KSCRKTLHGI CYGNFLHSSI EKCFTCIFGP SLDTKWSKFQ DLMMIRKVFR FLVRKKKGF PASITELIDS FINVEDQNNE VKERVAFALF VFFLDETLCL DNGGKPSQTI RYVTSSVLVD VKGIVIPNTR K QLNVNHEY KWHFTTSSPK AESFYQEVLP NSRKQVESWL QDITNLRKVY SEALS |
-Macromolecule #2: Histone H3
Macromolecule | Name: Histone H3 / type: protein_or_peptide / ID: 2 / Details: GenBank:CAD89679.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 15.30393 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA |
-Macromolecule #3: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 3 / Details: GenBank:NP_001087926.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 11.263231 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG |
-Macromolecule #4: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 4 / Details: GenBank:CAD89676.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.978241 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK |
-Macromolecule #5: Histone H2B
Macromolecule | Name: Histone H2B / type: protein_or_peptide / ID: 5 / Details: GenBank:CAD89678.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.524752 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK |
-Macromolecule #6: Widom 601 DNA (146-MER)
Macromolecule | Name: Widom 601 DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 45.27484 KDa |
Sequence | String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA) |
-Macromolecule #7: Widom 601 DNA (146-MER)
Macromolecule | Name: Widom 601 DNA (146-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 44.85657 KDa |
Sequence | String: (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String: (DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA) (DA)(DA) (DC)(DG)(DC)(DA)(DC)(DG)(DT) (DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC) (DC)(DC)(DC) (DC)(DG)(DC)(DG)(DT)(DT) (DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA) (DA)(DG)(DG)(DG) (DG)(DA)(DT)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC) (DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DC)(DA) (DT)(DC)(DC) (DT)(DG)(DT) |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.8 mg/mL |
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Buffer | pH: 7.5 / Details: 20mM Tris 7.5, 50mM NaCl, 1mM DTT, 1mM EDTA |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8cww: |