[English] 日本語
Yorodumi
- EMDB-14554: Mot1:TBP - product state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14554
TitleMot1:TBP - product state
Map datamain map
Sample
  • Complex: Mot1:TBP complex after DNA release
    • Protein or peptide: Mot1:TBP complex
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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
DepositionMar 17, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 31, 2023-
Current statusMay 31, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14554.png

Downloads & links

-
Map

FileDownload / File: emd_14554.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.6207245 - 1.8629292
Average (Standard dev.)0.0010030072 (±0.04531129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 296.52002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14554_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_14554_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_14554_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Mot1:TBP complex after DNA release

EntireName: Mot1:TBP complex after DNA release
Components
  • Complex: Mot1:TBP complex after DNA release
    • Protein or peptide: Mot1:TBP complex

-
Supramolecule #1: Mot1:TBP complex after DNA release

SupramoleculeName: Mot1:TBP complex after DNA release / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)

-
Macromolecule #1: Mot1:TBP complex

MacromoleculeName: Mot1:TBP complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATRLDRLVT ILETGSTRLI RDTAVNQLAD WQKQHPEELF NLLSRVVPYL RHKDWETRTT AAKAIGKIIE NAPLYDPNAG QDEAAPEPTN GSFEVKKEEE KDVLEQDNFF RLESLDVATI VKYGRPLLRG GPVDYNLAAL DPQKRLAHLK KTLNGRLGLL GRVFEDEEMP ...String:
MATRLDRLVT ILETGSTRLI RDTAVNQLAD WQKQHPEELF NLLSRVVPYL RHKDWETRTT AAKAIGKIIE NAPLYDPNAG QDEAAPEPTN GSFEVKKEEE KDVLEQDNFF RLESLDVATI VKYGRPLLRG GPVDYNLAAL DPQKRLAHLK KTLNGRLGLL GRVFEDEEMP VEQIASPITP NDAAGANGVG RQDGASNDNQ SQAIDESKMS ARQLNVLKRK RKREAQKAAQ GKSGFGDLSL RRSTTAGSDA FGEDTPMPDA DSKKNKLAEY FSLDRPENTE EDTKIVSEFK GPVLPIKSEI EADDSLEGAE WPFERLCEFL KVDLFDPQWE TRHGAAMGLR EVIRVHGAGA GRRRGKTRKE NNDLNRQWLD DLAYRLLCVL MLDKFTDYSS DTSVAPIRET VGQTLGAVLR HISVESVHAI YRLLYCMVTQ EDLPSEQNMW AVCHGGMVGL RYVVAVRKDL LLQDGDMIDG VVRCVMQGLG DIDDDVRSVS AATLIPMAKE FVMMRRSALD SLINIVWESL SNLGDDLSAS TGKIMDLLAT LCSFPEVLEA MKVSASQDEE RSFTLLVPRL YPFLRHTITS VRLAVLKALM TFANLGGETS QGWLNGRILR LIFQNIIVER DQDTLNMSLE LWTTLVRRLA ARDPAILADE FEAHAEPMMQ LALHPIGVPR HPIPMNPALF QKPSGGTYSL PGASQTNSRR SSPPEGERAT KRRRKSTKAE DVAPSTHTHD VDGHMIQGEV DLVGVDVLIR SRISAAKAMG LIMSFIPTPR LASYDTAVLQ ALSSPYASTQ LAAAMVIDEY AKNCSTPEVA SRFIEPLQKI IDLERPSHYR DLVTYVQRVR SASQQLINLF RDHGKVSQGK LPTLAVVVQG EPEAGPGAFS IANAEKVVNE DFERLKRLMA PGQRLIALPQ LNEAREQTVE VIEEAKAAKE ARDARIKAAA ACALVAMKVL PKKPSPLIKA IMDSIKTEEN QELQSRSAAT IARLVQLFTE SGRRGPAEKV VANLVKFSCV EVAETPEFPI HAHKTNVILS MQKEEDRVDH PDAVKYAREA KAARITRRGA KEALEILSKN FGAELLERVP TLRTFMEEPL VRAFSGDLPP EARDPENAFG QEIVDAMSVI RTMTPTLHPA LHPFVMQQVP LVIKALRSDL SVFRYMAAKC MATICSVITV DGMTALVEKV LPSINNPLDL SFRQGAIEVI YHLIAVMGDA ILPYVIFLIV PVLGRMSDSD NQIRLIATTS FATLVKLVPL EAGIPDPPGL SEELLKGRDR ERTFIAQLLD PKKIEPFKIP VAIKAELRSY QQEGVNWLAF LNKYHLHGIL CDDMGLGKTL QTICIVASDH HQRAEEFART GAPEVRKLPS LIICPPTLSG HWQQEIKTYA PFLTVTAYVG SPAERRAMKD SLDKTDIVIT SYDVCRNDID VIEKYNWNYC VLDEGHLIKN PKAKITLAVK RLTSNHRLIL TGTPIQNNVL ELWSLFDFLM PGFLGAEKVF LDRFAKPIAN SRYSKASSKE QEAGALAIEA LHKQVLPFLL RRLKEEVLND LPPKILQNYY CDLSDLQRKL FEDFTKREGK KITETAGRDD KEAKQHIFQA LQYMRKLCNS PALVMKPGHK AYEDTQKYLA KHGTTLEDPI HAPKLGALRD LLVDCGIGVE GQESSDPLYT PIKPHRALIF CQMKEMLDMV QNTVLKQMLP SVSYLRLDGS VEANKRQDIV NKFNSDPSYD VLLLTTSVGG LGLNLTGADT VIFVEHDWNP QKDLQAMDRA HRIGQKKVVN VYRIITRGTL EEKILSLQRF KIDVASTVVN QQNAGLATMD TDQILDLFNL GESGPSLITD NKESIEGREE DMVDIETGDV RRPGKKAAWL EGLGELWDNA QYEESFDLDG FLKTMQAAAW SHPQFEK MG SSHHHHHHSS GENLYFQGHM EAIQTHPANA AQAKAFTAPG SLSFPGGASE IANSTAPT N GASNGGQQQG VQATSGAGVT PATPAATPGA GPAGPSGITP TLQNIVATVN LDCRLDLKT IALHARNAEY NPKRFAAVIM RIREPKTTAL IFASGKMVVT GAKSEDDSKL ASRKYARIIQ KLGFNAKFT DFKIQNIVGS CDIKFPIRLE GLASKHHNFS SYEPELFPGL IYRMIKPKIV L LIFVSGKI VLTGAKVREE IYQAFEMIYP VLQDFRKV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 ATP-gamma-S before SEC and before grid preparation. 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..

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 44.0 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

+
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 117066
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more