+Open data
-Basic information
Entry | Database: PDB / ID: 6jpq | ||||||||||||||||||
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Title | CryoEM structure of Abo1 hexamer - ADP complex | ||||||||||||||||||
Components | Uncharacterized AAA domain-containing protein C31G5.19 | ||||||||||||||||||
Keywords | CHAPERONE / 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 | ||||||||||||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.44 Å | ||||||||||||||||||
Authors | Cho, C. / Jang, J. / Song, J.J. | ||||||||||||||||||
Funding support | Korea, Republic Of, 5items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6jpq.cif.gz | 670.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jpq.ent.gz | 514.3 KB | Display | PDB format |
PDBx/mmJSON format | 6jpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jpq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6jpq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6jpq_validation.xml.gz | 92.7 KB | Display | |
Data in CIF | 6jpq_validation.cif.gz | 140.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/6jpq ftp://data.pdbj.org/pub/pdb/validation_reports/jp/6jpq | HTTPS FTP |
-Related structure data
Related structure data | 9870MC 0800C 9871C 9872C 6jpuC 6jq0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Abo1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Saccharomyces (fungus) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.02 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.14_3260:phenix.real_space_refine) / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 4.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53582 / Symmetry type: POINT |
Refinement | Cross valid method: THROUGHOUT |
Displacement parameters | Biso max: 760.86 Å2 / Biso mean: 331.2868 Å2 / Biso min: 123.35 Å2 |