|Entry||Database: EMDB / ID: EMD-9354|
|Title||Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2|
|Sample||Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2|
|Biological species||Xenopus laevis (African clawed frog)|
|Method||single particle reconstruction / cryo EM / Resolution: 3.9 Å|
|Authors||Armache J-P / Gamarra N / Johnson SL / Wu S / Leonard JD / Narlikar GJ / Cheng Y|
|Funding support|| United States, 5 items |
|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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_9354.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.2156 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Additional map: Final map, unsharpened
|Annotation||Final map, unsharpened|
|Projections & Slices|
-Half map: Half map1
|Projections & Slices|
-Half map: Half map 2
-Entire Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9...
|Entire||Name: Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2|
Number of components: 1
-Component #1: protein, Cryo-EM structure of singly-bound SNF2h-nucleosome compl...
|Protein||Name: Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2|
Recombinant expression: No
|Mass||Theoretical: 340 MDa|
|Source||Species: Xenopus laevis (African clawed frog)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Strain: BL21(DE3)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temperature: 295.15 K / Humidity: 100 %|
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..
-Electron microscopy imaging
Model: Tecnai Polara / Image courtesy: FEI Company
|Imaging||Microscope: FEI POLARA 300|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 27513 |
Details: Frames were motion corrected using MotionCor2 with dose-weighting
|3D reconstruction||Algorithm: BACK PROJECTION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement protocol: flexible / Refinement space: REAL|
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