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Open data
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Basic information
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Title | Cryo-EM structure of doubly-bound SNF2h-nucleosome complex | |||||||||||||||
![]() | Double-bound SNF2h-nucleosome structure (cryoSPARC local refinement) | |||||||||||||||
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![]() | nucleosome / chromatin remodeler / ISWI / SNF2h / DNA BINDING PROTEIN-DNA complex | |||||||||||||||
Function / homology | ![]() histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / B-WICH complex / NURF complex ...histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / B-WICH complex / NURF complex / rDNA heterochromatin formation / chromatin silencing complex / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / negative regulation of transcription by RNA polymerase I / positive regulation of transcription by RNA polymerase I / regulation of DNA replication / ATP-dependent activity, acting on DNA / pericentric heterochromatin / heterochromatin formation / nucleosome binding / condensed chromosome / Deposition of new CENPA-containing nucleosomes at the centromere / helicase activity / positive regulation of DNA replication / cellular response to leukemia inhibitory factor / DNA-templated transcription initiation / 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 / 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 / histone binding / chromatin remodeling / protein heterodimerization activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
![]() | Chio US / Palovcak E / Armache JP / Narlikar GJ / Cheng Y | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 108.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 30.8 KB 30.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 106.9 KB | ||
Filedesc metadata | ![]() | 8.5 KB | ||
Others | ![]() ![]() | 200.2 MB 200.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v6vMC ![]() 8v4yC ![]() 8v7lC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Double-bound SNF2h-nucleosome structure (cryoSPARC local refinement) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8468 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_43002_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_43002_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : ATP-dependent chromatin remodeler SNF2h in complex with nucleosome
+Supramolecule #1: ATP-dependent chromatin remodeler SNF2h in complex with nucleosome
+Supramolecule #2: Nucleosome with Xenopus laevis histones
+Supramolecule #3: SNF2h
+Macromolecule #1: Histone H3.2
+Macromolecule #2: Histone H4
+Macromolecule #3: Histone H2A type 1
+Macromolecule #4: Histone H2B
+Macromolecule #7: SWI/SNF-related matrix-associated actin-dependent regulator of ch...
+Macromolecule #5: Widom 601 DNA (147-mer) with 60 base pairs flanking DNA (reverse ...
+Macromolecule #6: Widom 601 DNA (147-mer) with 60 base pairs flanking DNA (forward ...
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 Component:
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 | ||||||||||||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||||||||||||||
Details | 100 nM nucleosome with 500 nM SNF2h |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |