+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9353 | ||||||||||||||||||
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Title | Cryo-EM structure of SNF2h doubly-bound to the nucleosome | ||||||||||||||||||
Map data | Map in the pdb world, flipped handedness and repositioned to correspond to the deposited pdb | ||||||||||||||||||
Sample |
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Biological species | Xenopus laevis (African clawed frog) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.4 Å | ||||||||||||||||||
Authors | Armache J-P / Gamarra N / Johnson SL / Wu S / Leonard JD / Narlikar GJ / Cheng Y | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Elife / Year: 2019 Title: Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome. Authors: Jean Paul Armache / Nathan Gamarra / Stephanie L Johnson / John D Leonard / Shenping Wu / Geeta J Narlikar / Yifan Cheng / Abstract: The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome ...The SNF2h remodeler slides nucleosomes most efficiently as a dimer, yet how the two protomers avoid a tug-of-war is unclear. Furthermore, SNF2h couples histone octamer deformation to nucleosome sliding, but the underlying structural basis remains unknown. Here we present cryo-EM structures of SNF2h-nucleosome complexes with ADP-BeF that capture two potential reaction intermediates. In one structure, histone residues near the dyad and in the H2A-H2B acidic patch, distal to the active SNF2h protomer, appear disordered. The disordered acidic patch is expected to inhibit the second SNF2h protomer, while disorder near the dyad is expected to promote DNA translocation. The other structure doesn't show octamer deformation, but surprisingly shows a 2 bp translocation. FRET studies indicate that ADP-BeF predisposes SNF2h-nucleosome complexes for an elemental translocation step. We propose a model for allosteric control through the nucleosome, where one SNF2h protomer promotes asymmetric octamer deformation to inhibit the second protomer, while stimulating directional DNA translocation. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9353.map.gz | 74.6 MB | EMDB map data format | |
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Header (meta data) | emd-9353-v30.xml emd-9353.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_9353.png | 388.3 KB | ||
Others | emd_9353_additional.map.gz emd_9353_additional_1.map.gz emd_9353_half_map_1.map.gz emd_9353_half_map_2.map.gz | 50.3 MB 50.3 MB 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9353 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9353 | HTTPS FTP |
-Validation report
Summary document | emd_9353_validation.pdf.gz | 78.4 KB | Display | EMDB validaton report |
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Full document | emd_9353_full_validation.pdf.gz | 77.5 KB | Display | |
Data in XML | emd_9353_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9353 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9353 | HTTPS FTP |
-Related structure data
Related structure data | 9351C 9352C 9354C 9355C 9356C 6ne3C C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_9353.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map in the pdb world, flipped handedness and repositioned to correspond to the deposited pdb | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Final map, unsharpened, original handedness and position
File | emd_9353_additional.map | ||||||||||||
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Annotation | Final map, unsharpened, original handedness and position | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Final map, unsharpened, original handedness and position
File | emd_9353_additional_1.map | ||||||||||||
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Annotation | Final map, unsharpened, original handedness and position | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 1, original handedness and position
File | emd_9353_half_map_1.map | ||||||||||||
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Annotation | half-map 1, original handedness and position | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map 2, original handedness and position
File | emd_9353_half_map_2.map | ||||||||||||
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Annotation | half-map 2, original handedness and position | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+...
Entire | Name: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+2 and SHL-2, collected using scintillator-based camera |
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Components |
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-Supramolecule #1: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+...
Supramolecule | Name: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+2 and SHL-2, collected using scintillator-based camera type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) |
Molecular weight | Theoretical: 340 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK I Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 ...Details: 2.5 ul of nucleosome-443 SNF2h complexes were applied to a glow discharged Quantifoil holey carbon grid (1.2 um hole size, 400 mesh), blotted in a Vitrobot Mark I (FEI Company) using 6 seconds blotting at 100% humidity, and then plunge-frozen in liquid ethane cooled by liquid nitrogen.. |
Details | This sample was monodisperse |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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