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- EMDB-9353: Cryo-EM structure of SNF2h doubly-bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-9353
TitleCryo-EM structure of SNF2h doubly-bound to the nucleosome
Map dataMap in the pdb world, flipped handedness and repositioned to correspond to the deposited pdb
Sample
  • Complex: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+2 and 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: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9353.png

Downloads & links

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Map

FileDownload / File: emd_9353.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
Voxel sizeX=Y=Z: 1.2 Å
Density
Contour LevelBy AUTHOR: 1.3 / Movie #1: 0.9
Minimum - Maximum-1.3858436 - 3.8330925
Average (Standard dev.)0.011104753 (±0.1624069)
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-1.3863.8330.011

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Supplemental data

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Additional map: Final map, unsharpened, original handedness and position

Fileemd_9353_additional.map
AnnotationFinal map, unsharpened, original handedness and position
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Histogram (log scale)

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Additional map: Final map, unsharpened, original handedness and position

Fileemd_9353_additional_1.map
AnnotationFinal map, unsharpened, original handedness and position
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 1, original handedness and position

Fileemd_9353_half_map_1.map
Annotationhalf-map 1, original handedness and position
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map 2, original handedness and position

Fileemd_9353_half_map_2.map
Annotationhalf-map 2, original handedness and position
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+...

EntireName: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+2 and SHL-2, collected using scintillator-based camera
Components
  • Complex: 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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Supramolecule #1: Cryo-EM structure of SNF2h doubly-bound to the nucleosome at SHL+...

SupramoleculeName: 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
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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Image recordingFilm or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 25.0 e/Å2
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
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
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: 57060

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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