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- PDB-7zke: Mot1:TBP:DNA - pre-hydrolysis state -

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Basic information

Entry
Database: PDB / ID: 7zke
TitleMot1:TBP:DNA - pre-hydrolysis state
Components
  • (DNA (36-MER)) x 2
  • Helicase-like protein
  • Putative tata-box binding proteinTATA-binding protein
KeywordsTRANSCRIPTION / Swi2/Snf2 protein / remodeler / transcription initiation
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / TBP-class protein binding / helicase activity / DNA-templated transcription initiation / ATP hydrolysis activity / DNA binding / ATP binding / nucleus
Similarity search - Function
Mot1, central domain / Mot1, ATP-binding domain / Domain of unknown function (DUF3535) / TATA-binding protein-associated factor Mot1 / TATA-box binding protein, eukaryotic / : / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. ...Mot1, central domain / Mot1, ATP-binding domain / Domain of unknown function (DUF3535) / TATA-binding protein-associated factor Mot1 / TATA-box binding protein, eukaryotic / : / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / TBP domain superfamily / Helicase conserved C-terminal domain / Armadillo-like helical / helicase superfamily c-terminal domain / 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 / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA / DNA (> 10) / Helicase-like protein / Putative tata-box binding protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWoike, 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
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
CitationJournal: 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
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 31, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (36-MER)
B: DNA (36-MER)
D: Putative tata-box binding protein
E: Helicase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,1907
Polymers263,6734
Non-polymers5183
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8860 Å2
ΔGint-45 kcal/mol
Surface area79450 Å2
MethodPISA

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Components

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DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (36-MER)


Mass: 11155.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#2: DNA chain DNA (36-MER)


Mass: 11008.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)

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Protein , 2 types, 2 molecules DE

#3: Protein Putative tata-box binding protein / TATA-binding 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
#4: Protein Helicase-like 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

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mot1:TBP:DNA complex in pre-hydrolysis conformation / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: Rosetta (DE3)
Buffer solutionpH: 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
IDConc.NameBuffer-ID
120 mMHEPES1
260 mMsodium chloride1
35 mMmagnesium chloride1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283 K
Details: Incubation on the grid for 20 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177422 / Symmetry type: POINT

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