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Yorodumi- PDB-8siu: Origin Recognition Complex Associated (ORCA) protein bound to Orc2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8siu | |||||||||
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Title | Origin Recognition Complex Associated (ORCA) protein bound to Orc2 | |||||||||
Components |
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Keywords | PROTEIN BINDING / chromatin binding / ORC binding | |||||||||
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 / chromatin organization / DNA replication / chromosome, telomeric region / centrosome / chromatin binding / chromatin / nucleolus / nucleoplasm / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Bleichert, F. / Ekundayo, B.E. | |||||||||
Funding support | United States, European Union, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8siu.cif.gz | 246.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8siu.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 8siu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8siu_validation.pdf.gz | 441 KB | Display | wwPDB validaton report |
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Full document | 8siu_full_validation.pdf.gz | 442.5 KB | Display | |
Data in XML | 8siu_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 8siu_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/8siu ftp://data.pdbj.org/pub/pdb/validation_reports/si/8siu | HTTPS FTP |
-Related structure data
Related structure data | 8siyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42230.711 Da / Num. of mol.: 1 / Mutation: K646R,T647R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Lrwd1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A140UHX1 | ||||
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#2: Protein | Mass: 11570.101 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Orc2, Orc2l / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q75PQ8 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.2 M ammonium sulfate, 100 mM MES pH 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979092 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979092 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.51 Å / Num. obs: 45458 / % possible obs: 99.8 % / Redundancy: 39 % / Biso Wilson estimate: 22.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2577 / CC1/2: 0.505 / % possible all: 97.4 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.8→45.51 Å / SU ML: 0.1869 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 21.1448 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.51 Å
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Refine LS restraints |
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LS refinement shell |
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