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- EMDB-9749: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state -

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Basic information

Entry
Database: EMDB / ID: EMD-9749
TitleStructure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Map dataStructure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Sample
  • Complex: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Function / homology
Function and homology information


positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity / ATP-dependent activity, acting on DNA / nucleosomal DNA binding ...positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / cellular response to amino acid starvation / transcription initiation-coupled chromatin remodeling / histone reader activity / helicase activity / lysine-acetylated histone binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / structural constituent of chromatin / nucleosome / double-strand break repair / nucleosome assembly / RNA polymerase II-specific DNA-binding transcription factor binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Helicase/SANT-associated domain ...Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H2B / Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsLi M / Xia X
CitationJournal: Nature / Year: 2019
Title: Mechanism of DNA translocation underlying chromatin remodelling by Snf2.
Authors: Meijing Li / Xian Xia / Yuanyuan Tian / Qi Jia / Xiaoyu Liu / Ying Lu / Ming Li / Xueming Li / Zhucheng Chen /
Abstract: Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the ...Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme. Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes, which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear. Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeF. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeF triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.
History
DepositionDec 13, 2018-
Header (metadata) releaseApr 3, 2019-
Map releaseApr 3, 2019-
UpdateApr 3, 2019-
Current statusApr 3, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.055
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  • Surface view with fitted model
  • Atomic models: PDB-6iy3
  • Surface level: 0.055
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9749.png

Downloads & links

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Map

FileDownload / File: emd_9749.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 200 pix.
= 264. Å		1.32 Å/pix.
x 200 pix.
= 264. Å		1.32 Å/pix.
x 200 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.15814479 - 0.2899687
Average (Standard dev.)0.00066869456 (±0.010152452)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1580.2900.001

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Supplemental data

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Sample components

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Entire : Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state

EntireName: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
Components
  • Complex: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state

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Supramolecule #1: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state

SupramoleculeName: Structure of Snf2-MMTV-A nucleosome complex at shl-2 in ADP state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 300 KDa

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.8 µm / Calibrated magnification: 2250 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 2250
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

6700

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154645
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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