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- EMDB-43005: Cryo-EM structure of doubly-bound SNF2h-nucleosome complex (confo... -
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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 (conformation 2) | |||||||||||||||
![]() | doubly-bound SNF2h nucleosome variability component 2B (cryoSPARC local refinement) | |||||||||||||||
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Function / homology | ![]() histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / : / B-WICH complex ...histone octamer slider activity / RSF complex / ACF complex / WICH complex / negative regulation of mitotic chromosome condensation / CHRAC / NoRC complex / : / : / B-WICH complex / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | 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 | ![]() | 107.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.7 KB 27.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.7 KB | Display | ![]() |
Images | ![]() | 100 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 200.2 MB 200.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8v4yC ![]() 8v6vC ![]() 8v7lC C: citing same article ( |
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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
File | ![]() | ||||||||||||||||||||
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Annotation | doubly-bound SNF2h nucleosome variability component 2B (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 B
File | emd_43005_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_43005_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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 1.1
+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 (forward ...
+Macromolecule #6: Widom 601 DNA (147-mer) with 60 base pairs flanking DNA (reverse ...
-Experimental details
-Structure determination
Method | ![]() |
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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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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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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 66.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |