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Yorodumi- PDB-8v4y: Cryo-EM structure of singly-bound SNF2h-nucleosome complex with S... -
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-Basic information
Entry | Database: PDB / ID: 8v4y | |||||||||||||||
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Title | Cryo-EM structure of singly-bound SNF2h-nucleosome complex with SNF2h at inactive SHL2 (conformation 1) | |||||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / nucleosome / chromatin remodeler / ISWI / SNF2h / DNA BINDING PROTEIN-DNA complex | |||||||||||||||
Function / homology | Function and homology information RSF complex / histone octamer slider activity / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / NURF complex / B-WICH complex / rDNA heterochromatin formation ...RSF complex / histone octamer slider activity / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / NURF complex / B-WICH complex / rDNA heterochromatin formation / chromatin silencing complex / DNA methylation-dependent constitutive heterochromatin formation / ATP-dependent chromatin remodeler activity / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase III / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / nucleosome binding / ATP-dependent activity, acting on DNA / pericentric heterochromatin / condensed chromosome / antiviral innate immune response / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / heterochromatin formation / fibrillar center / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / site of double-strand break / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Chio, U.S. / Palovcak, E. / Armache, J.P. / Narlikar, G.J. / Cheng, Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2024 Title: Functionalized graphene-oxide grids enable high-resolution cryo-EM structures of the SNF2h-nucleosome complex without crosslinking. Authors: Un Seng Chio / Eugene Palovcak / Anton A A Smith / Henriette Autzen / Elise N Muñoz / Zanlin Yu / Feng Wang / David A Agard / Jean-Paul Armache / Geeta J Narlikar / Yifan Cheng / Abstract: Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the ...Single-particle cryo-EM is widely used to determine enzyme-nucleosome complex structures. However, cryo-EM sample preparation remains challenging and inconsistent due to complex denaturation at the air-water interface (AWI). Here, to address this issue, we develop graphene-oxide-coated EM grids functionalized with either single-stranded DNA (ssDNA) or thiol-poly(acrylic acid-co-styrene) (TAASTY) co-polymer. These grids protect complexes between the chromatin remodeler SNF2h and nucleosomes from the AWI and facilitate collection of high-quality micrographs of intact SNF2h-nucleosome complexes in the absence of crosslinking. The data yields maps ranging from 2.3 to 3 Å in resolution. 3D variability analysis reveals nucleotide-state linked conformational changes in SNF2h bound to a nucleosome. In addition, the analysis provides structural evidence for asymmetric coordination between two SNF2h protomers acting on the same nucleosome. We envision these grids will enable similar detailed structural analyses for other enzyme-nucleosome complexes and possibly other protein-nucleic acid complexes in general. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8v4y.cif.gz | 657.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8v4y.ent.gz | 516.7 KB | Display | PDB format |
PDBx/mmJSON format | 8v4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8v4y_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8v4y_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8v4y_validation.xml.gz | 53.6 KB | Display | |
Data in CIF | 8v4y_validation.cif.gz | 83.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/8v4y ftp://data.pdbj.org/pub/pdb/validation_reports/v4/8v4y | HTTPS FTP |
-Related structure data
Related structure data | 42977MC 8v6vC 8v7lC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 9 molecules AEBFCGDHW
#1: Protein | Mass: 15271.863 Da / Num. of mol.: 2 / Mutation: G102A, C110A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P84233 #2: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P62799 #3: Protein | Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P06897 #4: Protein | Mass: 13524.752 Da / Num. of mol.: 2 / Mutation: S29T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P02281 #7: Protein | | Mass: 122089.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA5, SNF2H, WCRF135 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta References: UniProt: O60264, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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-Widom 601 DNA (147-mer) with 60 base pairs flanking DNA ... , 2 types, 2 molecules IJ
#5: DNA chain | Mass: 64200.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#6: DNA chain | Mass: 63626.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#8: Chemical | ChemComp-ADP / |
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#9: Chemical | ChemComp-MG / |
#10: Chemical | ChemComp-BEF / |
-Details
Has ligand of interest | Y |
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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 |
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Molecular weight |
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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta(DE3) | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 Details: 12.5 mM HEPES-KOH, pH 7.5, 60 mM KCl, 5 mM MgCl2, 2 mM ADP, 2 mM BeSO4, 10 mM NaF, 1.5% glycerol | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 100 nM nucleosome with 500 nM SNF2h | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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 / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Image recording | Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Details: cryoSPARC Patch CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 8509125 Details: Particles picked using cryoSPARC's template picker with templates generated from a nucleosome. | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146702 Details: cryoSPARC non-uniform refinement. Gold-standard FSC determined by cryoSPARC using auto mask generation and tightening. Symmetry type: POINT |