[English] 日本語
Yorodumi- PDB-7uqj: Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7uqj | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / AAA+ ATPase / chromatin remodeler | ||||||
Function / homology | Function and homology information ATP-dependent histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / positive regulation of invasive growth in response to glucose limitation / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / CENP-A containing chromatin assembly / replication fork protection complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I ...ATP-dependent histone chaperone activity / sexual sporulation resulting in formation of a cellular spore / positive regulation of invasive growth in response to glucose limitation / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / CENP-A containing chromatin assembly / replication fork protection complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / rRNA transcription / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / chromosome, centromeric region / CENP-A containing nucleosome / structural constituent of chromatin / nucleosome / chromosome / chromatin organization / histone binding / chromatin remodeling / protein heterodimerization activity / chromatin binding / chromatin / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Wang, F. / Feng, X. / Li, H. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J Biol Chem / Year: 2023 Title: The Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly. Authors: Feng Wang / Xiang Feng / Qing He / Hua Li / Huilin Li / Abstract: The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to ...The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to promote nucleosome disassembly for DNA replication or RNA transcription. By cryo-EM analysis, here we show that Yta7 assembles a three-tiered hexamer with a top BRD tier, a middle AAA1 tier, and a bottom AAA2 tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix, termed BRD-interacting motif (BIM), of the largely disordered N-terminal region. The BIM motif is unique to the baker's yeast, and we show both BRD and BIM contribute to nucleosome recognition. We found that Yta7 binds both acetylated and nonacetylated H3 peptides but with a higher affinity for the unmodified peptide. This property is consistent with the absence of key residues of canonical BRDs involved in acetylated peptide recognition and the role of Yta7 in general nucleosome remodeling. Interestingly, the BRD tier exists in a spiral and a flat-ring form on top of the Yta7 AAA+ hexamer. The spiral is likely in a nucleosome-searching mode because the bottom BRD blocks the entry to the AAA+ chamber. The flat ring may be in a nucleosome disassembly state because the entry is unblocked and the H3 peptide has entered the AAA+ chamber and is stabilized by the AAA1 pore loops 1 and 2. Indeed, we show that the BRD tier is a flat ring when bound to the nucleosome. Overall, our study sheds light on the nucleosome disassembly by Yta7. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7uqj.cif.gz | 700.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7uqj.ent.gz | 520.4 KB | Display | PDB format |
PDBx/mmJSON format | 7uqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/7uqj ftp://data.pdbj.org/pub/pdb/validation_reports/uq/7uqj | HTTPS FTP |
---|
-Related structure data
Related structure data | 26696MC 7uqiC 7uqkC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 162182.969 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: YTA7, YGR270W / Plasmid: Yeast integrative vector pBS43 Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P40340, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #2: Protein/peptide | | Mass: 2680.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61830 #3: Chemical | ChemComp-ADP / | #4: Chemical | ChemComp-AGS / #5: Chemical | ChemComp-MG / Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of Yta7 with H3N tail / Type: COMPLEX Details: The translocation state of Histone 3 N-terminal peptide by Yta7 Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.93 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Plasmid: Yeast integrative vector pBS43 | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.6 Details: Solution was made fresh and detergent was added to solve preference orientation issue. | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The sample was a novel chromatin remodeler and a AAA+ ATPase. | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: The grids were doulbe blots / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: Blot 3S, blot forth 3 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 193 K / Temperature (min): 193 K |
Image recording | Electron dose: 65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) Details: A total of 75 frames were recorded for each micrograph stack. |
-Processing
EM software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 431065 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient |