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- EMDB-6883: Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state -

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Basic information

Entry
Database: EMDB / ID: EMD-6883
TitleStructure of Snf2-nucleosome complex at shl-2 in ADP BeFx state
Map data
Samplecomplex of snf2 and nucleosome in ADP BeFx state:
Transcription regulatory protein SNF2 / Histone H3.2 / Histone H4 / Histone H2A / Histone H2B 1.1 / (nucleic-acidNucleic acid) x 2 / (ligand) x 3
Function / homology
Function and homology information


positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / positive regulation of invasive growth in response to glucose limitation / positive regulation of mating type switching / sucrose catabolic process / nucleosome mobilization / strand invasion / SWI/SNF complex / rDNA binding / ATP-dependent chromatin remodeling ...positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of transcription from RNA polymerase II promoter in response to amino acid starvation / positive regulation of invasive growth in response to glucose limitation / positive regulation of mating type switching / sucrose catabolic process / nucleosome mobilization / strand invasion / SWI/SNF complex / rDNA binding / ATP-dependent chromatin remodeling / Hydrolases, Acting on acid anhydrides, Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-dependent ATPase activity / RNA polymerase II activating transcription factor binding / helicase activity / nucleosomal DNA binding / DNA-templated transcription, initiation / lysine-acetylated histone binding / double-strand break repair / nucleosome / DNA-dependent DNA replication / chromatin remodeling / protein heterodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Helicase superfamily 1/2, ATP-binding domain / AT hook, DNA-binding motif / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold ...Helicase superfamily 1/2, ATP-binding domain / AT hook, DNA-binding motif / Histone H2B / Bromodomain / Helicase, C-terminal / Histone H4 / Histone H2A / TATA box binding protein associated factor (TAF) / Histone H2A/H2B/H3 / Histone-fold / Helicase/SANT-associated domain / Glutamine-Leucine-Glutamine, QLQ / Bromodomain, conserved site / Histone H3/CENP-A / Histone H4, conserved site / P-loop containing nucleoside triphosphate hydrolase / Snf2, ATP coupling domain / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Bromodomain-like superfamily / SNF2-like, N-terminal domain superfamily / Core histone H2A/H2B/H3/H4 / SNF2 family N-terminal domain / SNF2-related, N-terminal domain / Helicase conserved C-terminal domain / Bromodomain / Histone H2A signature. / QLQ domain profile. / HSA domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Bromodomain profile. / Histone H3 signature 2. / Bromodomain signature. / Histone H2B signature. / Histone H3 signature 1. / Histone H4 signature. / C-terminus of histone H2A / Centromere kinetochore component CENP-T histone fold / Snf2-ATP coupling, chromatin remodelling complex / QLQ / HSA
Histone H2B 1.1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsLi M / Xia X / Liu X / Li X / Chen Z
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.
Validation ReportPDB-ID: 5z3v

SummaryFull reportAbout validation report
History
DepositionJan 8, 2018-
Header (metadata) releaseMay 22, 2019-
Map releaseMay 22, 2019-
UpdateMay 22, 2019-
Current statusMay 22, 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
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5z3v
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6883.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 160 pix.
= 211.2 Å
1.32 Å/pix.
x 160 pix.
= 211.2 Å
1.32 Å/pix.
x 160 pix.
= 211.2 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
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.22690275 - 0.3735661
Average (Standard dev.)0.0010115268 (±0.015617289)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z211.200211.200211.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2270.3740.001

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Supplemental data

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Sample components

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Entire complex of snf2 and nucleosome in ADP BeFx state

EntireName: complex of snf2 and nucleosome in ADP BeFx state / Number of components: 11

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Component #1: protein, complex of snf2 and nucleosome in ADP BeFx state

ProteinName: complex of snf2 and nucleosome in ADP BeFx state / Recombinant expression: No
MassTheoretical: 300 kDa
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #2: protein, Transcription regulatory protein SNF2

ProteinName: Transcription regulatory protein SNF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 85.802805 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Histone H3.2

ProteinName: Histone H3.2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.30393 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.978241 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.524752 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: nucleic-acid, DNA (167-MER)

nucleic acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC)(DC)(DT)(DG)(DA)(DA)(DG)(DC) (DT)(DT)(DG)(DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT)(DA)(DC)(DG)(DA)(DT)
MassTheoretical: 51.381758 kDa
SourceSpecies: synthetic construct (others)

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Component #8: nucleic-acid, DNA (167-MER)

nucleic acidName: DNA (167-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DT)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)
MassTheoretical: 51.723949 kDa
SourceSpecies: synthetic construct (others)

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Component #9: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Component #10: ligand, BERYLLIUM TRIFLUORIDE ION

LigandName: BERYLLIUM TRIFLUORIDE ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.600705 MDa

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Component #11: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE / Temperature: 281 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal), 22500.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1800.0 - 3200.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4247

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 101525
3D reconstructionSoftware: RELION / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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