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Yorodumi- EMDB-40522: Origin Recognition Complex Associated (ORCA) protein bound to H4K... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40522 | |||||||||
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Title | Origin Recognition Complex Associated (ORCA) protein bound to H4K20me3-nucleosome | |||||||||
Map data | unsharpened map | |||||||||
Sample |
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Keywords | chromatin binding / ORC binding / nucleosome / REPLICATION | |||||||||
Function / homology | Function and homology information Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / CDC6 association with the ORC:origin complex / Activation of the pre-replicative complex / Orc1 removal from chromatin / origin recognition complex / establishment of protein localization to chromatin / nuclear origin of replication recognition complex / inner kinetochore / methyl-CpG binding ...Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / CDC6 association with the ORC:origin complex / Activation of the pre-replicative complex / Orc1 removal from chromatin / origin recognition complex / establishment of protein localization to chromatin / nuclear origin of replication recognition complex / inner kinetochore / methyl-CpG binding / DNA replication origin binding / DNA replication initiation / heterochromatin / pericentric heterochromatin / methylated histone binding / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / DNA replication / chromosome, telomeric region / protein heterodimerization activity / centrosome / chromatin binding / chromatin / nucleolus / DNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) / Xenopus laevis (African clawed frog) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Bleichert F / Ekundayo BE | |||||||||
Funding support | United States, European Union, 2 items
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Citation | Journal: EMBO J / Year: 2023 Title: A dual role for the chromatin reader ORCA/LRWD1 in targeting the origin recognition complex to chromatin. Authors: Sumon Sahu / Babatunde E Ekundayo / Ashish Kumar / Franziska Bleichert / Abstract: Eukaryotic cells use chromatin marks to regulate the initiation of DNA replication. The origin recognition complex (ORC)-associated protein ORCA plays a critical role in heterochromatin replication ...Eukaryotic cells use chromatin marks to regulate the initiation of DNA replication. The origin recognition complex (ORC)-associated protein ORCA plays a critical role in heterochromatin replication in mammalian cells by recruiting the initiator ORC, but the underlying mechanisms remain unclear. Here, we report crystal and cryo-electron microscopy structures of ORCA in complex with ORC's Orc2 subunit and nucleosomes, establishing that ORCA orchestrates ternary complex assembly by simultaneously recognizing a highly conserved peptide sequence in Orc2, nucleosomal DNA, and repressive histone trimethylation marks through an aromatic cage. Unexpectedly, binding of ORCA to nucleosomes prevents chromatin array compaction in a manner that relies on H4K20 trimethylation, a histone modification critical for heterochromatin replication. We further show that ORCA is necessary and sufficient to specifically recruit ORC into chromatin condensates marked by H4K20 trimethylation, providing a paradigm for studying replication initiation in specific chromatin contexts. Collectively, our findings support a model in which ORCA not only serves as a platform for ORC recruitment to nucleosomes bearing specific histone marks but also helps establish a local chromatin environment conducive to subsequent MCM2-7 loading. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40522.map.gz | 92.3 MB | EMDB map data format | |
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Header (meta data) | emd-40522-v30.xml emd-40522.xml | 28.5 KB 28.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40522_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_40522.png | 94.1 KB | ||
Filedesc metadata | emd-40522.cif.gz | 7.3 KB | ||
Others | emd_40522_additional_1.map.gz emd_40522_additional_2.map.gz emd_40522_half_map_1.map.gz emd_40522_half_map_2.map.gz | 91 MB 97.2 MB 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40522 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40522 | HTTPS FTP |
-Validation report
Summary document | emd_40522_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_40522_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_40522_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_40522_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40522 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40522 | HTTPS FTP |
-Related structure data
Related structure data | 8siyMC 8siuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40522.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | unsharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: DeepEMhancer map
File | emd_40522_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: sharpened map
File | emd_40522_additional_2.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap
File | emd_40522_half_map_1.map | ||||||||||||
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Annotation | halfmap | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: halfmap
File | emd_40522_half_map_2.map | ||||||||||||
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Annotation | halfmap | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : ORCA-nucleosome (H4K20me3) complex
+Supramolecule #1: ORCA-nucleosome (H4K20me3) complex
+Supramolecule #2: Leucine-rich repeat and WD repeat-containing protein 1, Origin re...
+Supramolecule #3: Histone H3.2, Histone H4, Histone H2A, Histone H2B, Widom 601 DNA
+Macromolecule #1: Leucine-rich repeat and WD repeat-containing protein 1
+Macromolecule #2: Histone H3.2
+Macromolecule #3: Histone H4
+Macromolecule #4: Histone H2A
+Macromolecule #5: Histone H2B
+Macromolecule #8: Origin recognition complex subunit 2
+Macromolecule #6: Widom 601 DNA
+Macromolecule #7: Widom 601 DNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 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: 2.2 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |