+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Chaetomium thermophilum SETX - NPPC internal deletion | |||||||||
![]() | SETX-NPPC main map | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Williams RS / Appel CD | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 230.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 16.9 KB 16.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.2 KB | Display | ![]() |
Images | ![]() | 92.7 KB | ||
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 226.4 MB 226.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fthMC ![]() 8ftkC ![]() 8ftmC C: citing same article ( M: atomic model generated by this map |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | SETX-NPPC main map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8576 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: SETX-NPPC half map A
File | emd_29426_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | SETX-NPPC half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: SETX-NPPC half map B
File | emd_29426_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | SETX-NPPC half map B | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Chaemtomium thermophilum SETX in complex with ADP
Entire | Name: Chaemtomium thermophilum SETX in complex with ADP |
---|---|
Components |
|
-Supramolecule #1: Chaemtomium thermophilum SETX in complex with ADP
Supramolecule | Name: Chaemtomium thermophilum SETX in complex with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: 5'-3' RNA helicase-like protein
Macromolecule | Name: 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: ![]() |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 190.931109 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.9 |
---|---|
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |