+Open data
-Basic information
Entry | Database: PDB / ID: 7zke | |||||||||
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Title | Mot1:TBP:DNA - pre-hydrolysis state | |||||||||
Components |
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Keywords | TRANSCRIPTION / Swi2/Snf2 protein / remodeler / transcription initiation | |||||||||
Function / homology | Function and homology information ATP-dependent chromatin remodeler activity / RNA polymerase II general transcription initiation factor activity / TBP-class protein binding / helicase activity / DNA-templated transcription initiation / ATP hydrolysis activity / DNA binding / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | Chaetomium thermophilum (fungus) DNA molecule (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Woike, S. / Eustermann, S. / Jung, J. / Wenzl, S.J. / Hagemann, G. / Bartho, J.D. / Lammens, K. / Butryn, A. / Herzog, F. / Hopfner, K.-P. | |||||||||
Funding support | Germany, European Union, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Structural basis for TBP displacement from TATA box DNA by the Swi2/Snf2 ATPase Mot1. Authors: Stephan Woike / Sebastian Eustermann / James Jung / Simon Josef Wenzl / Götz Hagemann / Joseph Bartho / Katja Lammens / Agata Butryn / Franz Herzog / Karl-Peter Hopfner / Abstract: The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses adenosine triphosphate (ATP) to dissociate and reallocate the TATA box-binding protein (TBP) from and between ...The Swi2/Snf2 family transcription regulator Modifier of Transcription 1 (Mot1) uses adenosine triphosphate (ATP) to dissociate and reallocate the TATA box-binding protein (TBP) from and between promoters. To reveal how Mot1 removes TBP from TATA box DNA, we determined cryogenic electron microscopy structures that capture different states of the remodeling reaction. The resulting molecular video reveals how Mot1 dissociates TBP in a process that, intriguingly, does not require DNA groove tracking. Instead, the motor grips DNA in the presence of ATP and swings back after ATP hydrolysis, moving TBP to a thermodynamically less stable position on DNA. Dislodged TBP is trapped by a chaperone element that blocks TBP's DNA binding site. Our results show how Swi2/Snf2 proteins can remodel protein-DNA complexes through DNA bending without processive DNA tracking and reveal mechanistic similarities to RNA gripping DEAD box helicases and RIG-I-like immune sensors. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zke.cif.gz | 624.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zke.ent.gz | 504.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/7zke ftp://data.pdbj.org/pub/pdb/validation_reports/zk/7zke | HTTPS FTP |
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-Related structure data
Related structure data | 14762MC 7z7nC 7z8sC 7zb5C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 2 types, 2 molecules AB
#1: DNA chain | Mass: 11155.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
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#2: DNA chain | Mass: 11008.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others) |
-Protein , 2 types, 2 molecules DE
#3: Protein | Mass: 29676.973 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0042720 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SAL6 |
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#4: Protein | Mass: 211832.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0026210 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S6C0 |
-Non-polymers , 3 types, 3 molecules
#5: Chemical | ChemComp-MG / |
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#6: Chemical | ChemComp-ADP / |
#7: Chemical | ChemComp-BEF / |
-Details
Has ligand of interest | Y |
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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: Mot1:TBP:DNA complex in pre-hydrolysis conformation / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT | ||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||
Source (natural) | Organism: Chaetomium thermophilum (fungus) | ||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Rosetta (DE3) | ||||||||||||||||
Buffer solution | pH: 7.5 Details: Incubation with 1 mM ADP, 1 mM BeF2 and 5 mM NaF before blotting. 0.05% beta-octyl glucoside added before blotting. | ||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K Details: Incubation on the grid for 20 seconds before plunging. |
-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: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177422 / Symmetry type: POINT |