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- EMDB-9351: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9351
TitleCryo-EM structure of singly-bound SNF2h-nucleosome complex, with SNF2h bound at SHL+2
Map dataMap in the pdb world, flipped handedness and repositioned to correspond to the deposited pdb
Sample
  • Complex: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with SNF2h bound at SHL+2 collected using scintillator-based camera
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsArmache J-P / Gamarra N / Johnson SL / Wu S / Leonard JD / Narlikar GJ / Cheng Y
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood InstituteGM073767 United States
National Institutes of Health/National Heart, Lung, and Blood InstituteR01GM082893 United States
National Institutes of Health/National Heart, Lung, and Blood InstituteGM108455 United States
Other privateUCSF Program for Breakthrough Biomedical Research New Technology Award United States
National Institutes of Health/National Heart, Lung, and Blood Institute1S10OD020054 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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9351.png

Downloads & links

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Map

FileDownload / File: emd_9351.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap in the pdb world, flipped handedness and repositioned to correspond to the deposited pdb
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å		1.2 Å/pix.
x 300 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-1.2430753 - 4.3087187
Average (Standard dev.)0.008622844 (±0.15480639)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-1.2434.3090.009

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Supplemental data

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Additional map: Final map, unsharpened, flipped handedness

Fileemd_9351_additional.map
AnnotationFinal map, unsharpened, flipped handedness
Projections & Slices
AxesZYX

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Additional map: Final map, unsharpened, flipped handedness

Fileemd_9351_additional_1.map
AnnotationFinal map, unsharpened, flipped handedness
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1

Fileemd_9351_half_map_1.map
Annotationhalf-map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2

Fileemd_9351_half_map_2.map
Annotationhalf-map 2
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Sample components

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Entire : Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with ...

EntireName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with SNF2h bound at SHL+2 collected using scintillator-based camera
Components
  • Complex: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with SNF2h bound at SHL+2 collected using scintillator-based camera

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Supramolecule #1: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with ...

SupramoleculeName: Cryo-EM structure of singly-bound SNF2h-nucleosome complex, with SNF2h bound at SHL+2 collected using scintillator-based camera
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)
Molecular weightTheoretical: 340 kDa/nm

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen 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..
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 450322
Startup modelType of model: INSILICO MODEL / In silico model: Generated using cryosparc ab initio run
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 32233
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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