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Yorodumi- PDB-6iro: the crosslinked complex of ISWI-nucleosome in the ADP-bound state -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iro | ||||||
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Title | the crosslinked complex of ISWI-nucleosome in the ADP-bound state | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / chromatin remodelling / single particle CryO-EM / nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding ...Isw1b complex / Isw1 complex / Isw1a complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / ATP-dependent activity, acting on DNA / mRNA 3'-UTR binding / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / nucleosome assembly / response to heat / transcription cis-regulatory region binding / hydrolase activity / chromatin remodeling / protein heterodimerization activity / regulation of DNA-templated transcription / 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) Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Yan, L.J. / Wu, H. / Li, X.M. / Gao, N. / Chen, Z.C. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2019 Title: Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling. Authors: Lijuan Yan / Hao Wu / Xuemei Li / Ning Gao / Zhucheng Chen / Abstract: Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) ...Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 Å-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeF-bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6iro.cif.gz | 393.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iro.ent.gz | 292.3 KB | Display | PDB format |
PDBx/mmJSON format | 6iro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iro_validation.pdf.gz | 1018.9 KB | Display | wwPDB validaton report |
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Full document | 6iro_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6iro_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 6iro_validation.cif.gz | 67.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6iro ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6iro | HTTPS FTP |
-Related structure data
Related structure data | 9720MC 9718C 9719C 6jylC 6k1pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 9 molecules LAEBFCGDH
#1: Protein | Mass: 123184.609 Da / Num. of mol.: 1 / Mutation: D483K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: ISW1, YBR245C, YBR1633 / Production host: Escherichia coli K-12 (bacteria) References: UniProt: P38144, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement | ||||||
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#2: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A310TTQ1, UniProt: P84233*PLUS #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P62799 #4: Protein | Mass: 13978.241 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: hist1h2aj, LOC494591, XELAEV_18003602mg / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #5: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P02281 |
-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 51357.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) |
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#7: DNA chain | Mass: 51748.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli K-12 (bacteria) |
-Non-polymers , 1 types, 1 molecules
#8: Chemical | ChemComp-ADP / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 8.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: DIFFRACTION |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: REFMAC / Classification: refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168430 / Symmetry type: POINT |
Refinement | Cross valid method: THROUGHOUT |
Displacement parameters | Biso max: 349.53 Å2 / Biso mean: 114.8585 Å2 / Biso min: 35.58 Å2 |