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- EMDB-9354: Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9... -

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Entry
Database: EMDB / ID: EMD-9354
TitleCryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2
Map data
SampleCryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsArmache J-P / Gamarra N / Johnson SL / Wu S / Leonard JD / Narlikar GJ / Cheng Y
Funding support United States, 5 items
OrganizationGrant numberCountry
NIHGM073767 United States
NIHR01GM082893 United States
NIHGM108455 United States
UCSF Program for Breakthrough Biomedical ResearchNew Technology Award United States
NIH1S10OD020054 United States
CitationJournal: 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
DepositionDec 16, 2018-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateJul 17, 2019-
Current statusJul 17, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9354.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 256 pix.
= 311.194 Å
1.22 Å/pix.
x 256 pix.
= 311.194 Å
1.22 Å/pix.
x 256 pix.
= 311.194 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2156 Å
Density
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.28
Minimum - Maximum-0.5259982 - 1.4396586
Average (Standard dev.)0.001977517 (±0.05640302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 311.1936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21560156251.21560156251.2156015625
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z311.194311.194311.194
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.5261.4400.002

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Supplemental data

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Additional map: Final map, unsharpened

Fileemd_9354_additional.map
AnnotationFinal map, unsharpened
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: Half map1

Fileemd_9354_half_map_1.map
AnnotationHalf map1
Projections & Slices
AxesZYX

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Half map: Half map 2

Fileemd_9354_half_map_2.map
AnnotationHalf map 2
Projections & Slices
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Sample components

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Entire Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9...

EntireName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2
Number of components: 1

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Component #1: protein, Cryo-EM structure of singly-bound SNF2h-nucleosome compl...

ProteinName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex at 3.9A with SNF2h bound at SHL-2
Recombinant expression: No
MassTheoretical: 340 MDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21(DE3)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: 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..

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 41 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 27513
Details: Frames were motion corrected using MotionCor2 with dose-weighting
3D reconstructionAlgorithm: BACK PROJECTION / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL

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