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Open data
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Basic information
Entry | Database: PDB / ID: 8etw | ||||||
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Title | Class3 of INO80-Hexasome complex | ||||||
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![]() | DNA BINDING PROTEIN / chromatin remodeler / hexasome | ||||||
Function / homology | ![]() R2TP complex / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / DNA duplex unwinding / 3'-5' DNA helicase activity ...R2TP complex / regulation of TOR signaling / Swr1 complex / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / DNA duplex unwinding / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / chromosome, centromeric region / subtelomeric heterochromatin formation / enzyme regulator activity / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / histone binding / 5'-3' DNA helicase activity / chromosome, telomeric region / DNA helicase / transcription by RNA polymerase II / chromatin remodeling / protein stabilization / DNA repair / regulation of transcription by RNA polymerase II / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.64 Å | ||||||
![]() | Wu, H. / Munoz, E. / Gourdet, M. / Narlikar, G. / Cheng, Y.F. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 722.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28601MC ![]() 8etsC ![]() 8ettC ![]() 8etuC ![]() 8etvC ![]() 8eu2C ![]() 8eu9C ![]() 8eueC ![]() 8eufC ![]() 8eujC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-Chromatin-remodeling ... , 2 types, 2 molecules QS
#1: Protein | Mass: 54985.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() 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: 15881.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RuvB-like protein ... , 2 types, 6 molecules TVXUWY
#4: Protein | Mass: 48543.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 50153.898 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein / Protein/peptide / Non-polymers , 3 types, 8 molecules RZ![](data/chem/img/ADP.gif)
![](data/chem/img/ADP.gif)
#2: Protein | Mass: 86522.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein/peptide | Mass: 3531.075 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Chemical | ChemComp-ADP / |
-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 |
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Sample preparation
Component | Name: INO80-Hex / Type: COMPLEX / Entity ID: #1-#3, #6 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: OTHER |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233675 / Symmetry type: POINT |