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Yorodumi- PDB-8xjv: Structural basis for the linker histone H5-nucleosome binding and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xjv | |||||||||||||||||||||||||||||||||
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Title | Structural basis for the linker histone H5-nucleosome binding and chromatin compaction | |||||||||||||||||||||||||||||||||
Components |
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Keywords | GENE REGULATION / Chromatin Fiber / Histone / DNA / Linker Histone / Nucleosome / Epigenetics / Genome Folding / Interaction | |||||||||||||||||||||||||||||||||
Function / homology | Function and homology information negative regulation of DNA recombination / chromosome condensation / nucleosomal DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / double-stranded DNA binding / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | synthetic construct (others) Xenopus laevis (African clawed frog) Gallus gallus (chicken) | |||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||||||||||||||||||||
Authors | Li, W.Y. / Song, F. / Zhu, P. | |||||||||||||||||||||||||||||||||
Funding support | China, United States, 10items
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Citation | Journal: Cell Res / Year: 2024 Title: Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction. Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai ...Authors: Wenyan Li / Jie Hu / Feng Song / Juan Yu / Xin Peng / Shuming Zhang / Lin Wang / Mingli Hu / Jia-Cheng Liu / Yu Wei / Xue Xiao / Yan Li / Dongyu Li / Hui Wang / Bing-Rui Zhou / Linchang Dai / Zongjun Mou / Min Zhou / Haonan Zhang / Zheng Zhou / Huidong Zhang / Yawen Bai / Jin-Qiu Zhou / Wei Li / Guohong Li / Ping Zhu / Abstract: The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order ...The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo. | |||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xjv.cif.gz | 3.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8xjv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8xjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xjv_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8xjv_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8xjv_validation.xml.gz | 301.3 KB | Display | |
Data in CIF | 8xjv_validation.cif.gz | 516 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/8xjv ftp://data.pdbj.org/pub/pdb/validation_reports/xj/8xjv | HTTPS FTP |
-Related structure data
Related structure data | 38407MC 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
-DNA chain , 2 types, 2 molecules AuAv
#1: DNA chain | Mass: 651873.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: DNA chain | Mass: 660629.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
-Protein , 5 types, 108 molecules ABCDEFGHIKLajakalamanaoapaqarasatauAeJMNOPQ...
#3: Protein | Mass: 14109.436 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Details: H2A / Source: (gene. exp.) Xenopus laevis (African clawed frog) Gene: h2ac14.L, h2ac14, hist1h2aj, LOC494591, XELAEV_18003602mg Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13641.922 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281 #5: Protein | Mass: 15435.126 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1 #6: Protein | Mass: 11394.426 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799 #7: Protein | Mass: 21631.875 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P02259 |
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-Details
Has protein modification | N |
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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
Component |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: NITROGEN |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13670 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |