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- EMDB-14762: Mot1:TBP:DNA - pre-hydrolysis state -

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Basic information

Entry
Database: EMDB / ID: EMD-14762
TitleMot1:TBP:DNA - pre-hydrolysis state
Map datamain map
Sample
  • Complex: Mot1:TBP:DNA complex in pre-hydrolysis conformation
    • DNA: DNA (36-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: Putative tata-box binding protein
    • Protein or peptide: Helicase-like protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsSwi2/Snf2 protein / remodeler / transcription initiation / TRANSCRIPTION
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / TBP-class protein binding / DNA-templated transcription initiation / helicase activity / 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
Helicase-like protein / Putative tata-box binding protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWoike S / Eustermann S / Jung J / Wenzl SJ / Hagemann G / Bartho JD / Lammens K / Butryn A / Herzog F / Hopfner K-P
Funding support Germany, European Union, 2 items
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, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14762.png

Downloads & links

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Map

FileDownload / File: emd_14762.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 280 pix.
= 292.88 Å		1.05 Å/pix.
x 280 pix.
= 292.88 Å		1.05 Å/pix.
x 280 pix.
= 292.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.046 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-2.616191 - 4.501633
Average (Standard dev.)0.0042630425 (±0.09143184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 292.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14762_msk_1.map
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Mask #2

Fileemd_14762_msk_2.map
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Mask #3

Fileemd_14762_msk_3.map
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Additional map: composite map of N- and C-terminal focused refinements

Fileemd_14762_additional_1.map
Annotationcomposite map of N- and C-terminal focused refinements
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Half map: half map A

Fileemd_14762_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_14762_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Mot1:TBP:DNA complex in pre-hydrolysis conformation

EntireName: Mot1:TBP:DNA complex in pre-hydrolysis conformation
Components
  • Complex: Mot1:TBP:DNA complex in pre-hydrolysis conformation
    • DNA: DNA (36-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: Putative tata-box binding protein
    • Protein or peptide: Helicase-like protein
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Mot1:TBP:DNA complex in pre-hydrolysis conformation

SupramoleculeName: Mot1:TBP:DNA complex in pre-hydrolysis conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.155128 KDa
SequenceString:
(DC)(DG)(DG)(DC)(DC)(DG)(DG)(DG)(DC)(DG) (DC)(DC)(DC)(DG)(DG)(DC)(DA)(DT)(DG)(DG) (DC)(DG)(DG)(DC)(DC)(DT)(DA)(DT)(DA) (DA)(DA)(DA)(DG)(DG)(DG)(DC)

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Macromolecule #2: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 11.008016 KDa
SequenceString:
(DG)(DC)(DC)(DC)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DC)(DA)(DT) (DG)(DC)(DC)(DG)(DG)(DG)(DC)(DG)(DC) (DC)(DC)(DG)(DG)(DC)(DC)(DG)

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Macromolecule #3: Putative tata-box binding protein

MacromoleculeName: Putative tata-box binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 29.676973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGENLYFQG HMEAIQTHPA NAAQAKAFTA PGSLSFPGGA SEIANSTAPT NGASNGGQQQ GVQATSGAGV TPATPAATP GAGPAGPSGI TPTLQNIVAT VNLDCRLDLK TIALHARNAE YNPKRFAAVI MRIREPKTTA LIFASGKMVV T GAKSEDDS ...String:
MGSSHHHHHH SSGENLYFQG HMEAIQTHPA NAAQAKAFTA PGSLSFPGGA SEIANSTAPT NGASNGGQQQ GVQATSGAGV TPATPAATP GAGPAGPSGI TPTLQNIVAT VNLDCRLDLK TIALHARNAE YNPKRFAAVI MRIREPKTTA LIFASGKMVV T GAKSEDDS KLASRKYARI IQKLGFNAKF TDFKIQNIVG SCDIKFPIRL EGLASKHHNF SSYEPELFPG LIYRMIKPKI VL LIFVSGK IVLTGAKVRE EIYQAFEMIY PVLQDFRKV

UniProtKB: Putative tata-box binding protein

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Macromolecule #4: Helicase-like protein

MacromoleculeName: Helicase-like protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 211.832688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATRLDRLVT ILETGSTRLI RDTAVNQLAD WQKQHPEELF NLLSRVVPYL RHKDWETRTT AAKAIGKIIE NAPLYDPNAG QDEAAPEPT NGSFEVKKEE EKDVLEQDNF FRLESLDVAT IVKYGRPLLR GGPVDYNLAA LDPQKRLAHL KKTLNGRLGL L GRVFEDEE ...String:
MATRLDRLVT ILETGSTRLI RDTAVNQLAD WQKQHPEELF NLLSRVVPYL RHKDWETRTT AAKAIGKIIE NAPLYDPNAG QDEAAPEPT NGSFEVKKEE EKDVLEQDNF FRLESLDVAT IVKYGRPLLR GGPVDYNLAA LDPQKRLAHL KKTLNGRLGL L GRVFEDEE MPVEQIASPI TPNDAAGANG VGRQDGASND NQSQAIDESK MSARQLNVLK RKRKREAQKA AQGKSGFGDL SL RRSTTAG SDAFGEDTPM PDADSKKNKL AEYFSLDRPE NTEEDTKIVS EFKGPVLPIK SEIEADDSLE GAEWPFERLC EFL KVDLFD PQWETRHGAA MGLREVIRVH GAGAGRRRGK TRKENNDLNR QWLDDLAYRL LCVLMLDKFT DYSSDTSVAP IRET VGQTL GAVLRHISVE SVHAIYRLLY CMVTQEDLPS EQNMWAVCHG GMVGLRYVVA VRKDLLLQDG DMIDGVVRCV MQGLG DIDD DVRSVSAATL IPMAKEFVMM RRSALDSLIN IVWESLSNLG DDLSASTGKI MDLLATLCSF PEVLEAMKVS ASQDEE RSF TLLVPRLYPF LRHTITSVRL AVLKALMTFA NLGGETSQGW LNGRILRLIF QNIIVERDQD TLNMSLELWT TLVRRLA AR DPAILADEFE AHAEPMMQLA LHPIGVPRHP IPMNPALFQK PSGGTYSLPG ASQTNSRRSS PPEGERATKR RRKSTKAE D VAPSTHTHDV DGHMIQGEVD LVGVDVLIRS RISAAKAMGL IMSFIPTPRL ASYDTAVLQA LSSPYASTQL AAAMVIDEY AKNCSTPEVA SRFIEPLQKI IDLERPSHYR DLVTYVQRVR SASQQLINLF RDHGKVSQGK LPTLAVVVQG EPEAGPGAFS IANAEKVVN EDFERLKRLM APGQRLIALP QLNEAREQTV EVIEEAKAAK EARDARIKAA AACALVAMKV LPKKPSPLIK A IMDSIKTE ENQELQSRSA ATIARLVQLF TESGRRGPAE KVVANLVKFS CVEVAETPEF PIHAHKTNVI LSMQKEEDRV DH PDAVKYA REAKAARITR RGAKEALEIL SKNFGAELLE RVPTLRTFME EPLVRAFSGD LPPEARDPEN AFGQEIVDAM SVI RTMTPT LHPALHPFVM QQVPLVIKAL RSDLSVFRYM AAKCMATICS VITVDGMTAL VEKVLPSINN PLDLSFRQGA IEVI YHLIA VMGDAILPYV IFLIVPVLGR MSDSDNQIRL IATTSFATLV KLVPLEAGIP DPPGLSEELL KGRDRERTFI AQLLD PKKI EPFKIPVAIK AELRSYQQEG VNWLAFLNKY HLHGILCDDM GLGKTLQTIC IVASDHHQRA EEFARTGAPE VRKLPS LII CPPTLSGHWQ QEIKTYAPFL TVTAYVGSPA ERRAMKDSLD KTDIVITSYD VCRNDIDVIE KYNWNYCVLD EGHLIKN PK AKITLAVKRL TSNHRLILTG TPIQNNVLEL WSLFDFLMPG FLGAEKVFLD RFAKPIANSR YSKASSKEQE AGALAIEA L HKQVLPFLLR RLKEEVLNDL PPKILQNYYC DLSDLQRKLF EDFTKREGKK ITETAGRDDK EAKQHIFQAL QYMRKLCNS PALVMKPGHK AYEDTQKYLA KHGTTLEDPI HAPKLGALRD LLVDCGIGVE GQESSDPLYT PIKPHRALIF CQMKEMLDMV QNTVLKQML PSVSYLRLDG SVEANKRQDI VNKFNSDPSY DVLLLTTSVG GLGLNLTGAD TVIFVEHDWN PQKDLQAMDR A HRIGQKKV VNVYRIITRG TLEEKILSLQ RFKIDVASTV VNQQNAGLAT MDTDQILDLF NLGESGPSLI TDNKESIEGR EE DMVDIET GDVRRPGKKA AWLEGLGELW DNAQYEESFD LDGFLKTMQA AAWSHPQFEK

UniProtKB: Helicase-like protein

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #7: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
20.0 mMHEPES
60.0 mMsodium chloride
5.0 mMmagnesium chloride

Details: Incubation with 1 mM ADP, 1 mM BeF2 and 5 mM NaF before blotting. 0.05% beta-octyl glucoside added before blotting.
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP
Details: Incubation on the grid for 20 seconds before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6g7e

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 177422
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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