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- PDB-6jpq: CryoEM structure of Abo1 hexamer - ADP complex -

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Basic information

Entry
Database: PDB / ID: 6jpq
TitleCryoEM structure of Abo1 hexamer - ADP complex
ComponentsUncharacterized AAA domain-containing protein C31G5.19
KeywordsCHAPERONE / AAA+ ATPase Histone chaperone
Function / homology
Function and homology information


ATP-dependent H3-H4 histone complex chaperone activity / nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / chromatin / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities ...ATPase family AAA domain-containing protein ATAD2-like / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Bromodomain (BrD) profile. / Bromodomain-like superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATPase histone chaperone abo1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.44 Å
AuthorsCho, C. / Jang, J. / Song, J.J.
Funding support Korea, Republic Of, 5items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2016R1A2B3006293 Korea, Republic Of
National Research Foundation (NRF, Korea)2016K1A1A2912057 Korea, Republic Of
National Research Foundation (NRF, Korea)2018R1A6A7052113 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2015H1D3A1066116 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1D1A1B07047345 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of nucleosome assembly by the Abo1 AAA+ ATPase histone chaperone.
Authors: Carol Cho / Juwon Jang / Yujin Kang / Hiroki Watanabe / Takayuki Uchihashi / Seung Joong Kim / Koichi Kato / Ja Yil Lee / Ji-Joon Song /
Abstract: The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate ...The fundamental unit of chromatin, the nucleosome, is an intricate structure that requires histone chaperones for assembly. ATAD2 AAA+ ATPases are a family of histone chaperones that regulate nucleosome density and chromatin dynamics. Here, we demonstrate that the fission yeast ATAD2 homolog, Abo1, deposits histone H3-H4 onto DNA in an ATP-hydrolysis-dependent manner by in vitro reconstitution and single-tethered DNA curtain assays. We present cryo-EM structures of an ATAD2 family ATPase to atomic resolution in three different nucleotide states, revealing unique structural features required for histone loading on DNA, and directly visualize the transitions of Abo1 from an asymmetric spiral (ATP-state) to a symmetric ring (ADP- and apo-states) using high-speed atomic force microscopy (HS-AFM). Furthermore, we find that the acidic pore of ATP-Abo1 binds a peptide substrate which is suggestive of a histone tail. Based on these results, we propose a model whereby Abo1 facilitates H3-H4 loading by utilizing ATP.
History
DepositionMar 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Uncharacterized AAA domain-containing protein C31G5.19
B: Uncharacterized AAA domain-containing protein C31G5.19
C: Uncharacterized AAA domain-containing protein C31G5.19
D: Uncharacterized AAA domain-containing protein C31G5.19
E: Uncharacterized AAA domain-containing protein C31G5.19
F: Uncharacterized AAA domain-containing protein C31G5.19


Theoretical massNumber of molelcules
Total (without water)817,3656
Polymers817,3656
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Uncharacterized AAA domain-containing protein C31G5.19


Mass: 136227.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC31G5.19 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14114

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Abo1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces (fungus)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.02 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: (1.14_3260:phenix.real_space_refine) / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53582 / Symmetry type: POINT
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 760.86 Å2 / Biso mean: 331.2868 Å2 / Biso min: 123.35 Å2

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