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- EMDB-6834: Architecture of SWI/SNF remodeling complex -

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Basic information

Entry
Database: EMDB / ID: EMD-6834
TitleArchitecture of SWI/SNF remodeling complex
Map data
Sample
  • Complex: SWI/SNF
Function / homology
Function and homology information


carbon catabolite activation of transcription / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / : / : / : / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex ...carbon catabolite activation of transcription / RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / : / : / : / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / NuA3b histone acetyltransferase complex / NuA3a histone acetyltransferase complex / NuA3 histone acetyltransferase complex / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / : / Platelet degranulation / HDACs deacetylate histones / DNA strand invasion / rDNA binding / transcription factor TFIIF complex / mediator complex / nucleosome array spacer activity / histone H3K14ac reader activity / Ino80 complex / RSC-type complex / nucleosome disassembly / SUMOylation of chromatin organization proteins / ATP-dependent chromatin remodeler activity / SWI/SNF complex / nucleosomal DNA binding / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / nuclear chromosome / positive regulation of transcription by RNA polymerase I / NuA4 histone acetyltransferase complex / histone H4 reader activity / histone reader activity / RNA polymerase II preinitiation complex assembly / maturation of LSU-rRNA / transcription initiation-coupled chromatin remodeling / cellular response to amino acid starvation / helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / chromatin DNA binding / double-strand break repair via homologous recombination / DNA-templated DNA replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair / heterochromatin formation / chromatin organization / histone binding / transcription by RNA polymerase II / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / chromatin remodeling / DNA repair / hydrolase activity / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / ATP binding / nucleus / cytosol
Similarity search - Function
: / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / : / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / YEATS ...: / Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 / Chromatin remodelling complex Rsc7/Swp82 subunit / SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14 / : / SMARCC, C-terminal / SWIRM-associated region 1 / SNF5/SMARCB1/INI1 / SNF5 / SMARCB1 / INI1 / YEATS / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / : / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / ARID DNA-binding domain / ARID DNA-binding domain superfamily / ARID/BRIGHT DNA binding domain / ARID domain profile. / BRIGHT, ARID (A/T-rich interaction domain) domain / ARID/BRIGHT DNA binding domain / Helicase/SANT-associated domain / HSA domain profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / SWIB/MDM2 domain superfamily / SANT domain profile. / SANT domain / Myb-like DNA-binding domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / NET domain / Bromodomain extra-terminal - transcription regulation / Actin / Actin family / Actin / Homeobox-like domain superfamily / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SWI/SNF chromatin-remodeling complex subunit SWI1 / SWI/SNF chromatin-remodeling complex subunit SNF5 / Transcription regulatory protein SNF6 / SWI/SNF chromatin-remodeling complex subunit SNF2 / SWI/SNF complex subunit SWI3 / Transcription initiation factor TFIID subunit 14 / Transcription regulatory protein SNF11 / SWI/SNF global transcription activator complex subunit SWP82 / Transcription regulatory protein SNF12 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 33.0 Å
AuthorsWang XJ / Cai G
CitationJournal: Protein Cell / Year: 2018
Title: Architecture of SWI/SNF chromatin remodeling complex.
Authors: Zhihui Zhang / Xuejuan Wang / Jiyu Xin / Zhenrui Ding / Sheng Liu / Qianglin Fang / Na Yang / Rui-Min Xu / Gang Cai /
History
DepositionOct 17, 2017-
Header (metadata) releaseApr 4, 2018-
Map releaseApr 4, 2018-
UpdateApr 4, 2018-
Current statusApr 4, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6834.png

Downloads & links

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Map

FileDownload / File: emd_6834.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.54 Å/pix.
x 112 pix.
= 396.48 Å		3.54 Å/pix.
x 112 pix.
= 396.48 Å		3.54 Å/pix.
x 112 pix.
= 396.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.2 / Movie #1: 1.2
Minimum - Maximum-1.7150004 - 4.311587
Average (Standard dev.)0.019963969 (±0.3280176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions112112112
Spacing112112112
CellA=B=C: 396.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.543.543.54
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z396.480396.480396.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS112112112
D min/max/mean-1.7154.3120.020

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Supplemental data

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Sample components

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Entire : SWI/SNF

EntireName: SWI/SNF
Components
  • Complex: SWI/SNF

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Supramolecule #1: SWI/SNF

SupramoleculeName: SWI/SNF / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 60203
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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