+Open data
-Basic information
Entry | Database: PDB / ID: 8euf | ||||||
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Title | Class2 of the INO80-Nucleosome complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/Hydrolase / Chromatin Remodeler / hexasome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-Hydrolase complex | ||||||
Function / homology | Function and homology information R2TP complex / Swr1 complex / regulation of TOR signaling / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / DNA duplex unwinding / NuA4 histone acetyltransferase complex ...R2TP complex / Swr1 complex / regulation of TOR signaling / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / DNA duplex unwinding / NuA4 histone acetyltransferase complex / 3'-5' DNA helicase activity / subtelomeric heterochromatin formation / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / 5'-3' DNA helicase activity / histone binding / DNA helicase / transcription by RNA polymerase II / chromosome, telomeric region / protein stabilization / chromatin remodeling / DNA repair / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 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 | 8euf.cif.gz | 749.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8euf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8euf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8euf_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8euf_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8euf_validation.xml.gz | 106.9 KB | Display | |
Data in CIF | 8euf_validation.cif.gz | 157.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/8euf ftp://data.pdbj.org/pub/pdb/validation_reports/eu/8euf | HTTPS FTP |
-Related structure data
Related structure data | 28613MC 8etsC 8ettC 8etuC 8etvC 8etwC 8eu2C 8eu9C 8eueC 8eujC 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
-Chromatin-remodeling ... , 2 types, 2 molecules QS
#1: Protein | Mass: 171693.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c References: UniProt: P53115, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#3: Protein | Mass: 18564.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32617 |
-Protein , 2 types, 2 molecules RZ
#2: Protein | Mass: 87682.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53946 |
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#6: Protein | Mass: 36210.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40154 |
-RuvB-like protein ... , 2 types, 6 molecules TVXUWY
#4: Protein | Mass: 50516.941 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q03940, DNA helicase #5: Protein | Mass: 50539.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12464, DNA helicase |
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-Non-polymers , 1 types, 6 molecules
#7: Chemical | ChemComp-ADP / |
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-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: CELL / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: INO80-Ncp / Type: COMPLEX / Entity ID: #1-#3, #6 / Source: NATURAL |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
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 FIELD / 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: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44535 / Symmetry type: POINT |