+Open data
-Basic information
Entry | Database: PDB / ID: 8euj | |||||||||
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Title | Class2 of the INO80-Nucleosome complex | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Chromatin Remodeler / hexasome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information nucleosome assembly / structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus (frog) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Wu, H. / Munoz, E. / Gourdet, M. / Narlikar, G. / Cheng, Y.F. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2023 Title: Reorientation of INO80 on hexasomes reveals basis for mechanistic versatility. Authors: Hao Wu / Elise N Muñoz / Laura J Hsieh / Un Seng Chio / Muryam A Gourdet / Geeta J Narlikar / Yifan Cheng / Abstract: Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report ...Unlike other chromatin remodelers, INO80 preferentially mobilizes hexasomes, which can form during transcription. Why INO80 prefers hexasomes over nucleosomes remains unclear. Here, we report structures of INO80 bound to a hexasome or a nucleosome. INO80 binds the two substrates in substantially different orientations. On a hexasome, INO80 places its ATPase subunit, Ino80, at superhelical location -2 (SHL -2), in contrast to SHL -6 and SHL -7, as previously seen on nucleosomes. Our results suggest that INO80 action on hexasomes resembles action by other remodelers on nucleosomes such that Ino80 is maximally active near SHL -2. The SHL -2 position also plays a critical role for nucleosome remodeling by INO80. Overall, the mechanistic adaptations used by INO80 for preferential hexasome sliding imply that subnucleosomal particles play considerable regulatory roles. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8euj.cif.gz | 320.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8euj.ent.gz | 241.5 KB | Display | PDB format |
PDBx/mmJSON format | 8euj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/8euj ftp://data.pdbj.org/pub/pdb/validation_reports/eu/8euj | HTTPS FTP |
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-Related structure data
Related structure data | 28614MC 8etsC 8ettC 8etuC 8etvC 8etwC 8eu2C 8eu9C 8eueC 8eufC M: map data used to model this data 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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-Components
-Protein , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 15403.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (frog) Gene: LOC121398065, LOC108703785, LOC121398067, XELAEV_18002543mg Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1 #2: Protein | Mass: 11394.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62798 #3: Protein | Mass: 14109.436 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (frog) Gene: LOC494591, h2ac14.L, hist1h2aj, hist1h2aj.L, XELAEV_18003602mg Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #4: Protein | Mass: 13655.948 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus (frog) / Gene: XENTR_v90029538mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8Y854 |
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-DNA chain , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 69840.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 70347.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Class2 Nucleosome of the INO80-Nucleosome complex / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Xenopus (frog) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: OTHER |
-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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm |
Image recording | Electron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44535 / Symmetry type: POINT |