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- EMDB-29440: SETX-Sen1N domain -

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Basic information

Entry
Database: EMDB / ID: EMD-29440
TitleSETX-Sen1N domain
Map dataSETX-Sen1N domain main map
Sample
  • Complex: Chaemtomium thermophilum SETX (Sen1N domain)
    • Protein or peptide: SETX
KeywordsHelicase / TRANSCRIPTION / DNA repair / RNA-DNA hybrid
Biological speciesChaetomium thermophilum (fungus) / Thermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.49 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)ES102765 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_29440.png

Downloads & links

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Map

FileDownload / File: emd_29440.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSETX-Sen1N domain main map
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.24911405 - 0.6176358
Average (Standard dev.)0.000100737896 (±0.011812844)
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-Sen1N domain half map B

Fileemd_29440_half_map_1.map
AnnotationSETX-Sen1N domain half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SETX-Sen1N domain half map A

Fileemd_29440_half_map_2.map
AnnotationSETX-Sen1N domain half map A
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 (Sen1N domain)

EntireName: Chaemtomium thermophilum SETX (Sen1N domain)
Components
  • Complex: Chaemtomium thermophilum SETX (Sen1N domain)
    • Protein or peptide: SETX

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Supramolecule #1: Chaemtomium thermophilum SETX (Sen1N domain)

SupramoleculeName: Chaemtomium thermophilum SETX (Sen1N domain) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus)

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Macromolecule #1: SETX

MacromoleculeName: SETX / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
SequenceString: MENNDLYQAA IGWYRAFED C PPELHLCC PK VDDDDYA TYD EPDVVD DSGV PVEEK KRRIS AYEE RFQNVY NLS ILLGLGK EV AGPWLDEW T RAVDSLLKK CDTCVRNWHR NRDPYLKAL H LSPEQVTY LQ SKLDEFD RQR ITEGLQ RAKA ILEQY ...String:
MENNDLYQAA IGWYRAFED C PPELHLCC PK VDDDDYA TYD EPDVVD DSGV PVEEK KRRIS AYEE RFQNVY NLS ILLGLGK EV AGPWLDEW T RAVDSLLKK CDTCVRNWHR NRDPYLKAL H LSPEQVTY LQ SKLDEFD RQR ITEGLQ RAKA ILEQY GPMST VKLV DHDMSA VLA LYEALCS LP YLARPEHQ P LFDFVFENT QRKKPLRMQG GIIPSMTLF L FDESPVRR RF AETAWEN RQP GSITAQ EWDW AISGR LADQI VSLS FNRLQT LPP GQKILRF WS GFLFILHA L SEKQIINSL RAMEVSPSIY FLALEHLGT N SDEALAMV LR ALQELME KSS KAFWQA LEQV PPNQL VEEIF KSAA FRPLLN KSL RPELLVT EG DSQVPALA A WMRALVRSL PSTSWSDLCE TSLRHLFET F RSDQAVDQ SG RATCTLA GLV TLQQCL DGFL QQDSI DTGTG LIMV NQLLNR VVN YSEIIIR AA SLKPGDIY N VGISKAAMA IIHSALALDA KATEVEWAA L IAEKPVQD AV NRDSGAL WET FLEMLW AGQL GHFEL AKAML MATL RLRSIE QFI PKRKEQL KR ELDKFNKR Y QQQTTAIGK MLNRLTDFEP EVLDKLCSD P RGQTIHPI VS SLIHGED AIR EAGFQL LKAI TSESQ PSDAV GRML EVYFTP FLN AFSQAVD KL TATKDANS P WSHMIPILK CSDFVLTGLC DPSSGQLRR K VLTTEEHA AV KRWWECV WQA VDHSFR MMRI WHIKI DKKVM EDFC RDVMEL GNK LLAQDGV MA SSLAQESG E DAISKAMRE VLDPPRKCSY SLADMLQLR D KYLVMGII ET IKKLLSR LQE NEMnlp qrtr ghlds mlkkt kqrd grmdyl tkt nltdvqr ie llkalged a vieeqfmgt kpgdreakek eralkqskl d fskagisy sg dinehla qit pnfeky hkss lletl kkeep akpk apakls qqa ilanqqq ik eararera e karrdaeai akakalragk tipgegsgl q siagvrgk dh apvvkde imv gsssed egdd ddddd vinra ktks kkiwde aer rrlELEA EK LRGPVKKM K ILRSAKDMR ARLIPPMDVL HQAILEWDI F HEGNDPPN GY RCGNVSD TYP DPYSYK QTFF PLLIN EAWRS FVTA KDETTS KPF GIKVLSR MT VDKFMEVT A AVPAQISKD RGLTEGDIVI ISKGEDPLN Q PQELHCLS RI WKTTYKK DTV EVVYRL NAKG NQILP ALTPG SEFQ VVKITN MTT IEREYAA LE SLQYYDLM D EILKAQPSP MLTFGDEAIK AVMDNYQLN P GQARAILN AK ENDGFTL IQG PPGTGK TKTI VAMVG CLLTG VLKS SNTGav qis rpgagpt ng tapskklL V CAPSNAAVD ELVLRLKAGV KTMNGTFHK I EVLRLGRS DV INAAVKD VTL Delvka rmda elskn sspse rdql hkeage ika klaeiRP QL DAARLSDD R ASAMKLQRE FDELKRRQAH IGAKIDADK A SGNTYARE TE IKRRQIQ QEI LDKAQV LCAT LSGSG HEMFK NLNV EFETVI IDE AAQCVEL SA LIPLKYGC N KCILVGDPK QLPPTVLSQS AAKYGYDQS L FVRMQKNH PK DVHLLDM QYR MHPEIS RFPS KEFYE GLLQD GADM ARLRLQ PWH QSVLLGP YR FFDVKGSQ E RGPKNQSLV NEEEVKVAMQ LYMRFRSDY R DIDLTGKI GI ITPYKAQ LQR LRQKFV ERYG ESITE QIEFN TTDA FQGREC EII IFSCVRA SP TGGIGFMT D IRRMNVGLT RARSSLWILG DSRALVQGE F WAKLIEDA KQ RDRYTNG NIM ALLSQP GPRV SLESl akqys vpva pvarsk edv emhdtpr ts esippamp y rgsgiggln ergeattptt rggelpiiq s tdgsagkk rp rdaneen rpa fdpaka ssaf wftqt tgigi gidr sfcdgs fga gssnpsa ss atatpsss g tf

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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: 4.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74760
FSC plot (resolution estimation)

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