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- EMDB-29439: Chaetomium thermophilum SETX (Full-length) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-29439
TitleChaetomium thermophilum SETX (Full-length)
Map dataSETX-FL main map
Sample
  • Complex: Chaemtomium thermophilum SETX (Full-length)
    • Protein or peptide: 5'-3' RNA helicase-like protein
KeywordsHelicase / TRANSCRIPTION / DNA repair / RNA-DNA hybrid
Function / homology
Function and homology information


Helicase Sen1, N-terminal / SEN1 N terminal / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-3' RNA helicase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / Thermochaetoides thermophila DSM 1495 (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.56 Å
AuthorsWilliams RS / Appel CD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ES102765 United States
CitationJournal: Mol Cell / Year: 2023
Title: Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2.
Authors: C Denise Appel / Oya Bermek / Venkata P Dandey / Makayla Wood / Elizabeth Viverette / Jason G Williams / Jonathan Bouvette / Amanda A Riccio / Juno M Krahn / Mario J Borgnia / R Scott Williams /
Abstract: The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for ...The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron microscopy (cryo-EM) reconstructions reveal an elongated inchworm-like architecture. Sen1 is composed of an amino terminal helical repeat Sen1 N-terminal (Sen1N) regulatory domain that is flexibly linked to its C-terminal SF1B helicase motor core (Sen1) via an intrinsically disordered tether. In an autoinhibited state, the Sen1 domain regulates substrate engagement by promoting occlusion of the RNA substrate-binding cleft. The X-ray structure of an activated Sen1 engaging single-stranded RNA and ADP-SO shows that the enzyme encircles RNA and implicates a single-nucleotide power stroke in the Sen1 RNA translocation mechanism. Together, our data unveil dynamic protein-protein and protein-RNA interfaces underpinning helicase regulation and inactivation of human SETX activity by RNA-binding-deficient mutants in ataxia with oculomotor apraxia 2 neurodegenerative disease.
History
DepositionJan 12, 2023-
Header (metadata) releaseOct 25, 2023-
Map releaseOct 25, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29439.png

Downloads & links

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Map

FileDownload / File: emd_29439.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSETX-FL main map
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.14466652 - 0.47985584
Average (Standard dev.)0.0003435709 (±0.012856779)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SETX-FL half map A

Fileemd_29439_half_map_1.map
AnnotationSETX-FL half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SETX-FL half map B

Fileemd_29439_half_map_2.map
AnnotationSETX-FL half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chaemtomium thermophilum SETX (Full-length)

EntireName: Chaemtomium thermophilum SETX (Full-length)
Components
  • Complex: Chaemtomium thermophilum SETX (Full-length)
    • Protein or peptide: 5'-3' RNA helicase-like protein

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Supramolecule #1: Chaemtomium thermophilum SETX (Full-length)

SupramoleculeName: Chaemtomium thermophilum SETX (Full-length) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: 5'-3' RNA helicase-like protein

MacromoleculeName: 5'-3' RNA helicase-like protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 223.790109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENNDLYQAA IGWYRAFEDC PPELHLCCPK VDDDDYATYD EPDVVDDSGV PVEEKKRRIS AYEERFQNVY NLSILLGLGK EVAGPWLDE WTRAVDSLLK KCDTCVRNWH RNRDPYLKAL HLSPEQVTYL QSKLDEFDRQ RITEGLQRAK AILEQYGPMS T VKLVDHDM ...String:
MENNDLYQAA IGWYRAFEDC PPELHLCCPK VDDDDYATYD EPDVVDDSGV PVEEKKRRIS AYEERFQNVY NLSILLGLGK EVAGPWLDE WTRAVDSLLK KCDTCVRNWH RNRDPYLKAL HLSPEQVTYL QSKLDEFDRQ RITEGLQRAK AILEQYGPMS T VKLVDHDM SAVLALYEAL CSLPYLARPE HQPLFDFVFE NTQRKKPLRM QGGIIPSMTL FLFDESPVRR RFAETAWENR QP GSITAQE WDWAISGRLA DQIVSLSFNR LQTLPPGQKI LRFWSGFLFI LHALSEKQII NSLRAMEVSP SIYFLALEHL GTN SDEALA MVLRALQELM EKSSKAFWQA LEQVPPNQLV EEIFKSAAFR PLLNKSLRPE LLVTEGDSQV PALAAWMRAL VRSL PSTSW SDLCETSLRH LFETFRSDQA VDQSGRATCT LAGLVTLQQC LDGFLQQDSI DTGTGLIMVN QLLNRVVNYS EIIIR AASL KPGDIYNVGI SKAAMAIIHS ALALDAKATE VEWAALIAEK PVQDAVNRDS GALWETFLEM LWAGQLGHFE LAKAML MAT LRLRSIEQFI PKRKEQLKRE LDKFNKRYQQ QTTAIGKMLN RLTDFEPEVL DKLCSDPRGQ TIHPIVSSLI HGEDAIR EA GFQLLKAITS ESQPSDAVGR MLEVYFTPFL NAFSQAVDKL TATKDANSPW SHMIPILKCS DFVLTGLCDP SSGQLRRK V LTTEEHAAVK RWWECVWQAV DHSFRMMRIW HIKIDKKVME DFCRDVMELG NKLLAQDGVM ASSLAQESGE DAISKAMRE VLDPPRKCSY SLADMLQLRD KYLVMGIIET IKKLLSRLQE NEMNLPQRTR GHLDSMLKKT KQRDGRMDYL TKTNLTDVQR IELLKALGE DAVIEEQFMG TKPGDREAKE KERALKQSKL DFSKAGISYS GDINEHLAQI TPNFEKYHKS SLLETLKKEE P AKPKAPAK LSQQAILANQ QQIKEARARE RAEKARRDAE AIAKAKALRA GKTIPGEGSG LQSIAGVRGK DHAPVVKDEI MV GSSSEDE GDDDDDDDVI NRAKTKSKKI WDEAERRRLE LEAEKLRGPV KKMKILRSAK DMRARLIPPM DVLHQAILEW DIF HEGNDP PNGYRCGNVS DTYPDPYSYK QTFFPLLINE AWRSFVTAKD ETTSKPFGIK VLSRMTVDKF MEVTAAVPAQ ISKD RGLTE GDIVIISKGE DPLNQPQELH CLSRIWKTTY KKDTVEVVYR LNAKGNQILP ALTPGSEFQV VKITNMTTIE REYAA LESL QYYDLMDEIL KAQPSPMLTF GDEAIKAVMD NYQLNPGQAR AILNAKENDG FTLIQGPPGT GKTKTIVAMV GCLLTG VLK SSNTGAVQIS RPGAGPTNGT APSKKLLVCA PSNAAVDELV LRLKAGVKTM NGTFHKIEVL RLGRSDVINA AVKDVTL DE LVKARMDAEL SKNSSPSERD QLHKEAGEIK AKLAEIRPQL DAARLSDDRA SAMKLQREFD ELKRRQAHIG AKIDADKA S GNTYARETEI KRRQIQQEIL DKAQVLCATL SGSGHEMFKN LNVEFETVII DEAAQCVELS ALIPLKYGCN KCILVGDPK QLPPTVLSQS AAKYGYDQSL FVRMQKNHPK DVHLLDMQYR MHPEISRFPS KEFYEGLLQD GADMARLRLQ PWHQSVLLGP YRFFDVKGS QERGPKNQSL VNEEEVKVAM QLYMRFRSDY RDIDLTGKIG IITPYKAQLQ RLRQKFVERY GESITEQIEF N TTDAFQGR ECEIIIFSCV RASPTGGIGF MTDIRRMNVG LTRARSSLWI LGDSRALVQG EFWAKLIEDA KQRDRYTNGN IM ALLSQPG PRVSLESLAK QYSVPVAPVA RSKEDVEMHD TPRTSESIPP AMPYRGSGIG GLNERGEATT PTTRGGELPI IQS TDGSAG KKRPRDANEE NRPAFDPAKA SSAFWFTQTT GIGIGIDRSF CDGSFGAGSS NPSASSATAT PSSSGTF

UniProtKB: 5'-3' RNA helicase-like protein

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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

BufferpH: 7.9
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29391
FSC plot (resolution estimation)

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