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Yorodumi- PDB-7e9f: Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e9f | |||||||||
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Title | Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / nucleosome / transcriptional silencing / chromatin | |||||||||
Function / homology | Function and homology information CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / Orc1 removal from chromatin / HDMs demethylate histones / HATs acetylate histones / maintenance of rDNA / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex ...CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / sexual sporulation resulting in formation of a cellular spore / Orc1 removal from chromatin / HDMs demethylate histones / HATs acetylate histones / maintenance of rDNA / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / SUMOylation of chromatin organization proteins / nuclear pre-replicative complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / replication fork protection complex / RMTs methylate histone arginines / silent mating-type cassette heterochromatin formation / positive regulation of transcription by RNA polymerase I / DNA replication origin binding / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / DNA replication initiation / nucleosome binding / CENP-A containing nucleosome / nucleosome assembly / structural constituent of chromatin / nucleosome / chromatin organization / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | |||||||||
Authors | Jiang, H. / Yu, C. / Liu, C.P. / Han, X. / Yu, Z. / Xu, R.M. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1 Authors: Jiang, H. / Yu, C. / Liu, C.P. / Han, X. / Yu, Z. / Xu, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e9f.cif.gz | 411.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9f.ent.gz | 303.7 KB | Display | PDB format |
PDBx/mmJSON format | 7e9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9f ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9f | HTTPS FTP |
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-Related structure data
Related structure data | 31030MC 7e9cC C: citing same article (ref.) M: map data used to model this data |
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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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-Components
-Protein , 5 types, 10 molecules AEBFCGDHKL
#1: Protein | Mass: 15146.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830 #2: Protein | Mass: 11395.390 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309 #3: Protein | Mass: 14013.177 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTA2, H2A2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / References: UniProt: P04912 #4: Protein | Mass: 14264.341 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / References: UniProt: P02294 #7: Protein | Mass: 25423.887 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ORC1, YML065W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54784 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 45145.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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#6: DNA chain | Mass: 45604.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3247: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119206 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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