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- EMDB-29426: Chaetomium thermophilum SETX - NPPC internal deletion -

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Basic information

Entry
Database: EMDB / ID: EMD-29426
TitleChaetomium thermophilum SETX - NPPC internal deletion
Map dataSETX-NPPC main map
Sample
  • Complex: Chaemtomium thermophilum SETX in complex with ADP
    • Protein or peptide: 5'-3' RNA helicase-like protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsHelicase / TRANSCRIPTION / DNA repair / RNA-DNA hybrid
Function / homology
Function and homology information


helicase activity / nucleotide binding
Similarity search - Function
Helicase Sen1, N-terminal / SEN1 N terminal / DNA2/NAM7 helicase, helicase domain / AAA domain / : / DNA2/NAM7-like helicase / 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: 3.17 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_29426.png

Downloads & links

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Map

FileDownload / File: emd_29426.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSETX-NPPC main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 343.04 Å		0.86 Å/pix.
x 400 pix.
= 343.04 Å		0.86 Å/pix.
x 400 pix.
= 343.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8576 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.2707534 - 3.0489736
Average (Standard dev.)-0.0001658626 (±0.04358486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 343.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: SETX-NPPC half map A

Fileemd_29426_half_map_1.map
AnnotationSETX-NPPC half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: SETX-NPPC half map B

Fileemd_29426_half_map_2.map
AnnotationSETX-NPPC 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 in complex with ADP

EntireName: Chaemtomium thermophilum SETX in complex with ADP
Components
  • Complex: Chaemtomium thermophilum SETX in complex with ADP
    • Protein or peptide: 5'-3' RNA helicase-like protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Chaemtomium thermophilum SETX in complex with ADP

SupramoleculeName: Chaemtomium thermophilum SETX in complex with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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
Details: engineered fragment: internal deletion and C-terminal truncation,engineered fragment: internal deletion and C-terminal truncation
Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Molecular weightTheoretical: 190.931109 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 TKPGLEVLFQ GPLEVLFQGP MKILRSAKDM RARLIPPMDV LHQAILEWDI FHEGNDPPNG Y RCGNVSDT YPDPYSYKQT FFPLLINEAW RSFVTAKDET TSKPFGIKVL SRMTVDKFME VTAAVPAQIS KDRGLTEGDI VI ISKGEDP LNQPQELHCL SRIWKTTYKK DTVEVVYRLN AKGNQILPAL TPGSEFQVVK ITNMTTIERE YAALESLQYY DLM DEILKA QPSPMLTFGD EAIKAVMDNY QLNPGQARAI LNAKENDGFT LIQGPPGTGK TKTIVAMVGC LLTGVLKSSN TGAV QISRP GAGPTNGTAP SKKLLVCAPS NAAVDELVLR LKAGVKTMNG TFHKIEVLRL GRSDVINAAV KDVTLDELVK ARMDA ELSK NSSPSERDQL HKEAGEIKAK LAEIRPQLDA ARLSDDRASA MKLQREFDEL KRRQAHIGAK IDADKASGNT YARETE IKR RQIQQEILDK AQVLCATLSG SGHEMFKNLN VEFETVIIDE AAQCVELSAL IPLKYGCNKC ILVGDPKQLP PTVLSQS AA KYGYDQSLFV RMQKNHPKDV HLLDMQYRMH PEISRFPSKE FYEGLLQDGA DMARLRLQPW HQSVLLGPYR FFDVKGSQ E RGPKNQSLVN EEEVKVAMQL YMRFRSDYRD IDLTGKIGII TPYKAQLQRL RQKFVERYGE SITEQIEFNT TDAFQGREC EIIIFSCVRA SPTGGIGFMT DIRRMNVGLT RARSSLWILG DSRALVQGEF WAKLIEDAKQ RDRYTNGNIM ALLSQPGPRV SLESLAKQ

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

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / 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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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: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 471395
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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