[English] 日本語
Yorodumi- EMDB-6700: Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6700 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome | |||||||||
Map data | Density map of Snf2-nucleosome complex with Snf2 binding to SHL2 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 4.69A. | |||||||||
Sample |
| |||||||||
Keywords | Snf2 / 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 / rDNA binding / DNA strand invasion / 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 / rDNA binding / DNA strand invasion / SWI/SNF complex / ATP-dependent chromatin remodeler activity / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / lysine-acetylated histone binding / cellular response to amino acid starvation / helicase activity / 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 / chromatin remodeling / hydrolase activity / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.69 Å | |||||||||
Authors | Li M / Liu X / Xia X / Cheng Z / Li X | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6700.map.gz | 4.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-6700-v30.xml emd-6700.xml | 21.4 KB 21.4 KB | Display Display | EMDB header |
Images | emd_6700.png | 139.5 KB | ||
Filedesc metadata | emd-6700.cif.gz | 7 KB | ||
Others | emd_6700_additional.map.gz | 49.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6700 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6700 | HTTPS FTP |
-Validation report
Summary document | emd_6700_validation.pdf.gz | 354.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_6700_full_validation.pdf.gz | 354.3 KB | Display | |
Data in XML | emd_6700_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_6700_validation.cif.gz | 7.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6700 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6700 | HTTPS FTP |
-Related structure data
Related structure data | 5x0yMC 6699C 5x0xC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_6700.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Density map of Snf2-nucleosome complex with Snf2 binding to SHL2 of the nucleosome. The map was sharpened by RELION post-processing, and the resolution was reported at 4.69A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: Unsharpened density map of Snf2-nucleosome complex with Snf2...
File | emd_6700_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Unsharpened density map of Snf2-nucleosome complex with Snf2 binding to SHL2 of the nucleosome. The resolution was reported at 7.18A. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : SHL2 complex
Entire | Name: SHL2 complex |
---|---|
Components |
|
-Supramolecule #1: SHL2 complex
Supramolecule | Name: SHL2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c |
-Macromolecule #1: Histone H3.2
Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 15.289904 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3.2 |
-Macromolecule #2: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 11.263231 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A
Macromolecule | Name: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Molecular weight | Theoretical: 13.978241 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK UniProtKB: Histone H2A |
-Macromolecule #4: Histone H2B 1.1
Macromolecule | Name: 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 weight | Theoretical: 13.524752 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK UniProtKB: Histone H2B 1.1 |
-Macromolecule #7: Transcription regulatory protein SNF2
Macromolecule | Name: 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 weight | Theoretical: 85.802805 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #5: DNA (167-MER)
Macromolecule | Name: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.381758 KDa |
Sequence | 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) ...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) |
-Macromolecule #6: DNA (167-MER)
Macromolecule | Name: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 51.723949 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
---|---|
Grid | Model: Quantifoil holey carbon grid / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: A cylinder initial model generated with SPIDER and the negative staining model |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 90725 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |