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- EMDB-6699: Complex of Snf2-Nucleosome complex with Snf2 bound to position +6... -

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Entry
Database: EMDB / ID: EMD-6699
TitleComplex of Snf2-Nucleosome complex with Snf2 bound to position +6 of the nucleosome
Map dataDensity map of Snf2-nucleosome complex with Snf2 binding to SHL6 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 3.97A.
Sample
  • Complex: SHL6 complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: Transcription regulatory protein SNF2
KeywordsSnf2 / nucleosome / chromatin remodeling / STRUCTURAL PROTEIN-HYDROLASE-DNA complex
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 / nucleosomal DNA binding / ATP-dependent activity, acting on DNA ...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 / nucleosomal DNA binding / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / lysine-acetylated histone binding / DNA-templated DNA replication / structural constituent of chromatin / double-strand break repair / nucleosome / 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 domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / Helicase/SANT-associated domain / HSA domain profile. ...Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / DNA binding domain with preference for A/T rich regions / Helicase/SANT-associated domain / HSA domain profile. / AT hook, DNA-binding motif / : / 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. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Helicase conserved C-terminal domain / Histone H3 signature 1. / 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. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 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 1.1 / Histone H2A type 1 / Transcription regulatory protein SNF2 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsLi M / Liu X / Xia X / Cheng Z / Li X
CitationJournal: Nature / Year: 2017
Title: Mechanism of chromatin remodelling revealed by the Snf2-nucleosome structure.
Authors: Xiaoyu Liu / Meijing Li / Xian Xia / Xueming Li / Zhucheng Chen /
Abstract: Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron ...Chromatin remodellers are helicase-like, ATP-dependent enzymes that alter chromatin structure and nucleosome positions to allow regulatory proteins access to DNA. Here we report the cryo-electron microscopy structure of chromatin remodeller Switch/sucrose non-fermentable (SWI2/SNF2) from Saccharomyces cerevisiae bound to the nucleosome. The structure shows that the two core domains of Snf2 are realigned upon nucleosome binding, suggesting activation of the enzyme. The core domains contact each other through two induced Brace helices, which are crucial for coupling ATP hydrolysis to chromatin remodelling. Snf2 binds to the phosphate backbones of one DNA gyre of the nucleosome mainly through its helicase motifs within the major domain cleft, suggesting a conserved mechanism of substrate engagement across different remodellers. Snf2 contacts the second DNA gyre via a positively charged surface, providing a mechanism to anchor the remodeller at a fixed position of the nucleosome. Snf2 locally deforms nucleosomal DNA at the site of binding, priming the substrate for the remodelling reaction. Together, these findings provide mechanistic insights into chromatin remodelling.
History
DepositionJan 23, 2017-
Header (metadata) releaseApr 19, 2017-
Map releaseApr 19, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0274
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0274
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  • Surface view with fitted model
  • Atomic models: PDB-5x0x
  • Surface level: 0.0274
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6699.png

Downloads & links

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Map

FileDownload / File: emd_6699.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of Snf2-nucleosome complex with Snf2 binding to SHL6 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 3.97A.
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0274 / Movie #1: 0.0274
Minimum - Maximum-0.09042521 - 0.13913299
Average (Standard dev.)0.0002603509 (±0.0036176634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.920337.920337.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0900.1390.000

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Supplemental data

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Additional map: Unsharpened density map of Snf2-nucleosome complex with Snf2...

Fileemd_6699_additional.map
AnnotationUnsharpened density map of Snf2-nucleosome complex with Snf2 binding to SHL6 of the nucleosome.The resolution was reported at 6.14A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SHL6 complex

EntireName: SHL6 complex
Components
  • Complex: SHL6 complex
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: Transcription regulatory protein SNF2

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Supramolecule #1: SHL6 complex

SupramoleculeName: SHL6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.848097 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK TQKKDGKKRR KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Transcription regulatory protein SNF2

MacromoleculeName: Transcription regulatory protein SNF2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 85.802805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AYIKLLDQTK DTRITHLLRQ TNAFLDSLTR AVKDQQKYTK EMIDSHIKEA SEEVDDLSMV PKMKDEEYDD DDDNSNVDYY NVAHRIKED IKKQPSILVG GTLKDYQIKG LQWMVSLFNN HLNGILADEM GLGKTIQTIS LLTYLYEMKN IRGPYLVIVP L STLSNWSS ...String:
AYIKLLDQTK DTRITHLLRQ TNAFLDSLTR AVKDQQKYTK EMIDSHIKEA SEEVDDLSMV PKMKDEEYDD DDDNSNVDYY NVAHRIKED IKKQPSILVG GTLKDYQIKG LQWMVSLFNN HLNGILADEM GLGKTIQTIS LLTYLYEMKN IRGPYLVIVP L STLSNWSS EFAKWAPTLR TISFKGSPNE RKAKQAKIRA GEFDVVLTTF EYIIKERALL SKVKWVHMII DEGHRMKNAQ SK LSLTLNT HYHADYRLIL TGTPLQNNLP ELWALLNFVL PKIFNSVKSF DEWFNTPFAN TGGQDKIELS EEETLLVIRR LHK VLRPFL LRRLKKDVEK ELPDKVEKVV KCKMSALQQI MYQQMLKYRR LFIGDQNNKK MVGLRGFNNQ IMQLKKICNH PFVF EEVED QINPTRETND DIWRVAGKFE LLDRILPKLK ATGHRVLIFF QMTQIMDIME DFLRYINIKY LRLDGHTKSD ERSEL LRLF NAPDSEYLCF ILSTRAGGLG LNLQTADTVI IFDTDWNPHQ DLQAQDRAHR IGQKNEVRIL RLITTNSVEE VILERA YKK LDIDGKVIQA GKFDNKSTSE EQEALLRSLL DAEEERRKKR ESGVEEEEEL KDSEINEILA RNDEEMAVLT RMDEDRS KK EEELGVKSRL LEKSELPDIY SRDIGAELKR EESESAAVYN GRGARERKTA TYNDNMSEEQ WLRQFEVSDD EKNDKQAR K QRTKKEDKSE AIDG

UniProtKB: Transcription regulatory protein SNF2

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Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.381758 KDa
SequenceString: (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) ...String:
(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)(DG)(DA)(DT)(DA)(DG)(DC)(DT)(DT)(DG) (DT)(DC)(DG)(DA)(DG)(DA)(DA) (DG)(DT) (DA)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.723949 KDa
SequenceString: (DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DT)(DA)(DC)(DT)(DT)(DC) (DT)(DC)(DG)(DA)(DC)(DA)(DA)(DG)(DC)(DT) (DA)(DT)(DC)(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)

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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
GridModel: Quantifoil holey carbon grid / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: A cylinder initial model generated with SPIDER and the negative staining model
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 90725

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