+Open data
-Basic information
Entry | Database: PDB / ID: 5z3v | ||||||
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Title | Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN/HYDROLASE/DNA / complex / nucleosome / chromatin remodeling / gene regulation / 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 / 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 / DNA strand invasion / rDNA binding / SWI/SNF complex / ATP-dependent chromatin remodeler activity / ATP-dependent activity, acting on DNA / nucleosomal DNA binding / cellular response to amino acid starvation / helicase activity / lysine-acetylated histone binding / 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 / 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Xenopus laevis (African clawed frog) synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.22 Å | ||||||
Authors | Li, M. / Xia, X. / Liu, X. / Li, X. / Chen, Z. | ||||||
Citation | Journal: 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. | ||||||
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 | 5z3v.cif.gz | 444.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z3v.ent.gz | 337.8 KB | Display | PDB format |
PDBx/mmJSON format | 5z3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5z3v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5z3v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5z3v_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 5z3v_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/5z3v ftp://data.pdbj.org/pub/pdb/validation_reports/z3/5z3v | HTTPS FTP |
-Related structure data
Related structure data | 6883MC 6879C 6880C 6882C 9748C 9749C 5z3lC 5z3oC 5z3uC 6iy2C 6iy3C 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 OAEBFCGDH
#1: Protein | Mass: 85802.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C / Variant: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) References: UniProt: P22082, 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233 #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 (E. coli) / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8 #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 (E. coli) / References: UniProt: P02281 |
-DNA chain , 2 types, 2 molecules IJ
#6: DNA chain | Mass: 51381.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#7: DNA chain | Mass: 51723.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#8: Chemical | ChemComp-ADP / |
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#9: Chemical | ChemComp-BEF / |
#10: Chemical | ChemComp-MG / |
-Details
Sequence details | Authors state that the sample sequence of chain D/H is conformed by DNA sequencing and consistents ...Authors state that the sample sequence of chain D/H is conformed by DNA sequencing and consistents with the literature (PDB code 3MVD) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: complex of snf2 and nucleosome in ADP BeFx state / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.3 MDa / Experimental value: NO |
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1800 nm / Calibrated defocus min: 1800 nm / Calibrated defocus max: 3200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 8 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 4247 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32 |
-Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101525 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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