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- PDB-9cat: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module -

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Basic information

Entry
Database: PDB / ID: 9cat
TitleDeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module
Components
  • (Chromatin-remodeling ...) x 2
  • (RuvB-like protein ...) x 2
  • Actin-related protein 5
  • Ino eighty subunit 2
KeywordsDNA BINDING PROTEIN / Chromatin Remodeler / nucleosome
Function / homology
Function and homology information


TTT Hsp90 cochaperone complex / R2TP complex / regulation of TOR signaling / Swr1 complex / Ino80 complex / telomere maintenance via recombination / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / regulation of metabolic process / 3'-5' DNA helicase activity ...TTT Hsp90 cochaperone complex / R2TP complex / regulation of TOR signaling / Swr1 complex / Ino80 complex / telomere maintenance via recombination / ATP-dependent chromatin remodeler activity / box C/D snoRNP assembly / regulation of metabolic process / 3'-5' DNA helicase activity / cellular response to stress / 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 / 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 / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / PAPA-1-like conserved region / PAPA-1 / : ...DBINO domain / DNA helicase Ino80 / DNA-binding domain / DBINO domain profile. / INO80 complex, subunit Ies6 / INO80 complex subunit B-like conserved region / INO80 complex, subunit Ies2 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWu, H. / Kaur, U. / Narlikar, G.J. / Cheng, Y.F.
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: 2025
Title: Autoinhibition imposed by a large conformational switch of INO80 regulates nucleosome positioning.
Authors: Upneet Kaur / Hao Wu / Yifan Cheng / Geeta J Narlikar /
Abstract: Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like ...Increasing the flanking DNA from 40 to 80 base pairs (bp) causes ~100-fold faster nucleosome sliding by INO80. A prevalent hypothesis posits that the Arp8 module within INO80 enables a ruler-like activity. Using cryogenic electron microscopy, we show that on nucleosomes with 40 bp of flanking DNA, the Arp8 module rotates 180° away from the DNA. Deleting the Arp8 module enables rapid sliding irrespective of flanking DNA length. Thus, rather than enabling a ruler-like activity, the Arp8 module acts as a brake on INO80 remodeling when flanking DNA is short. This autoinhibition-based mechanism has broad implications for understanding how primitive nucleosome mobilization enzymes may have evolved into sophisticated remodelers.
History
DepositionJun 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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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)619,88416
Polymers617,32110
Non-polymers2,5636
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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: 171693.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
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: 18564.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32617

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Protein , 2 types, 2 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 (brewer's yeast) / References: UniProt: P53946
#6: Protein Ino eighty subunit 2


Mass: 36210.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40154

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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: 50516.941 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03940, DNA helicase
#5: Protein RuvB-like protein 2 / RUVBL2 / TIP49-homology protein 2 / TIP49b homolog


Mass: 50539.367 Da / Num. of mol.: 3 / Fragment: residues 1-460 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12464, DNA helicase

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Non-polymers , 1 types, 6 molecules

#7: Chemical
ChemComp-ADP / ADENOSINE-5'-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
Has protein modificationN

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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: DeltaArp8 INO80 bound to S.c 0/40 nucleosome, INO80 Core Module
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
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 FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 47.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36091 / Symmetry type: POINT

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