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- PDB-8eu9: Class1 of the INO80-Nucleosome complex -

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Basic information

Entry
Database: PDB / ID: 8eu9
TitleClass1 of the INO80-Nucleosome complex
Components
  • (Chromatin-remodeling ...) x 2
  • (RuvB-like protein ...) x 2
  • Actin-related protein 5
  • Ino eighty subunit 2
KeywordsDNA 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 / 5'-3' DNA helicase activity / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity ...R2TP complex / Swr1 complex / regulation of TOR signaling / telomere maintenance via recombination / Ino80 complex / regulation of metabolic process / 5'-3' DNA helicase activity / box C/D snoRNP assembly / ATP-dependent chromatin remodeler activity / 3'-5' DNA helicase activity / NuA4 histone acetyltransferase complex / DNA duplex unwinding / subtelomeric heterochromatin formation / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / rRNA processing / histone binding / DNA helicase / transcription by RNA polymerase II / chromosome, telomeric region / protein stabilization / chromatin remodeling / DNA repair / chromatin / regulation of DNA-templated transcription / 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
DNA helicase Ino80 / DBINO domain profile. / DBINO domain / DNA-binding domain / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / PAPA-1-like conserved region / PAPA-1 / Vps72/YL1, C-terminal ...DNA helicase Ino80 / DBINO domain profile. / DBINO domain / DNA-binding domain / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / INO80 complex, subunit Ies6 / PAPA-1-like conserved region / PAPA-1 / Vps72/YL1, C-terminal / YL1 nuclear protein C-terminal domain / YL1 nuclear protein C-terminal domain / RuvB-like / RuvB-like, AAA-lid domain / RuvBL1/2, DNA/RNA binding domain / TIP49 P-loop domain / TIP49 AAA-lid domain / TIP49, P-loop domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Actin / Actin family / Actin / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chromatin-remodeling complex subunit IES6 / Ino eighty subunit 2 / Chromatin-remodeling ATPase INO80 / Actin-related protein 5 / RuvB-like protein 1 / RuvB-like protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWu, H. / Munoz, E. / Gourdet, M. / Cheng, Y.F. / Narlikar, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD) United States
CitationJournal: 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
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Q: Chromatin-remodeling ATPase INO80
R: Actin-related protein 5
S: Chromatin-remodeling complex subunit IES6
T: RuvB-like protein 1
U: RuvB-like protein 2
V: RuvB-like protein 1
W: RuvB-like protein 2
X: RuvB-like protein 1
Y: RuvB-like protein 2
Z: Ino eighty subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)457,86216
Polymers455,29910
Non-polymers2,5636
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Chromatin-remodeling ... , 2 types, 2 molecules QS

#1: Protein Chromatin-remodeling ATPase INO80 / Inositol-requiring protein 80


Mass: 56002.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
References: UniProt: P53115, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein Chromatin-remodeling complex subunit IES6 / Ino eighty subunit 6


Mass: 15392.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32617

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RuvB-like protein ... , 2 types, 6 molecules TVXUWY

#4: Protein RuvB-like protein 1 / RUVBL1 / TIP49-homology protein 1 / TIP49a homolog


Mass: 48543.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q03940, DNA helicase
#5: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 49019.773 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12464, DNA helicase

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Protein / Protein/peptide / Non-polymers , 3 types, 8 molecules RZ

#2: Protein Actin-related protein 5 / Actin-like protein ARP5


Mass: 87682.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53946
#6: Protein/peptide Ino eighty subunit 2


Mass: 3531.075 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
#7: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: INO80-Ncp / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2000 nm / Nominal defocus min: -1000 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22054 / Symmetry type: POINT

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