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Yorodumi- PDB-7kbf: H1.8 bound nucleosome isolated from metaphase chromosome in Xenop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kbf | |||||||||
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Title | H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / nucleosome / M phase / cell cycle / chromatin / Xenopus egg extract / H1 / Chromatosome / Linker histone | |||||||||
Function / homology | Function and homology information multicellular organism development / structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.42 Å | |||||||||
Authors | Arimura, Y. / Funabiki, H. | |||||||||
Funding support | United States, Japan, 2items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structural features of nucleosomes in interphase and metaphase chromosomes. Authors: Yasuhiro Arimura / Rochelle M Shih / Ruby Froom / Hironori Funabiki / Abstract: Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo- ...Structural heterogeneity of nucleosomes in functional chromosomes is unknown. Here, we devise the template-, reference- and selection-free (TRSF) cryo-EM pipeline to simultaneously reconstruct cryo-EM structures of protein complexes from interphase or metaphase chromosomes. The reconstructed interphase and metaphase nucleosome structures are on average indistinguishable from canonical nucleosome structures, despite DNA sequence heterogeneity, cell-cycle-specific posttranslational modifications, and interacting proteins. Nucleosome structures determined by a decoy-classifying method and structure variability analyses reveal the nucleosome structural variations in linker DNA, histone tails, and nucleosome core particle configurations, suggesting that the opening of linker DNA, which is correlated with H2A C-terminal tail positioning, is suppressed in chromosomes. High-resolution (3.4-3.5 Å) nucleosome structures indicate DNA-sequence-independent stabilization of superhelical locations ±0-1 and ±3.5-4.5. The linker histone H1.8 preferentially binds to metaphase chromatin, from which chromatosome cryo-EM structures with H1.8 at the on-dyad position are reconstituted. This study presents the structural characteristics of nucleosomes in chromosomes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kbf.cif.gz | 328.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kbf.ent.gz | 245.5 KB | Display | PDB format |
PDBx/mmJSON format | 7kbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kbf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7kbf_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7kbf_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 7kbf_validation.cif.gz | 77.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/7kbf ftp://data.pdbj.org/pub/pdb/validation_reports/kb/7kbf | HTTPS FTP |
-Related structure data
Related structure data | 22792MC 7kbdC 7kbeC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | |
EM raw data | EMPIAR-10691 (Title: Oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract (lot1) Data size: 1.3 TB Data #1: oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract lot1 [micrographs - multiframe] Data #2: oligo nucleosome fraction from metaphase chromosome in Xenopus egg extract lot1 [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 9 molecules AEBFCGDHK
#1: Protein | Mass: 15421.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P84233 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P62799 #3: Protein | Mass: 14883.174 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6DKE3 #4: Protein | Mass: 13965.265 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P02281 #7: Protein | | Mass: 29387.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: P15308 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 53114.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) |
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#6: DNA chain | Mass: 53083.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: H1.8 bound nucleosome isolated from metaphase chromosome in Xenopus egg extract (oligo fraction) Type: COMPLEX / Entity ID: all / Source: NATURAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Xenopus laevis (African clawed frog) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company | |||||||||||||||
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Microscopy | Model: FEI TALOS ARCTICA | |||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM | |||||||||||||||
Electron lens | Mode: BRIGHT FIELD | |||||||||||||||
Image recording |
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-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27383 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building |
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