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- EMDB-18288: CryoEM structure of a S. Cerevisiae Ski238 complex bound to RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-18288
TitleCryoEM structure of a S. Cerevisiae Ski238 complex bound to RNA
Map data
Sample
  • Complex: Ski238 polyU RNA
    • Protein or peptide: Antiviral helicase SKI2
    • Protein or peptide: Superkiller protein 3
    • Protein or peptide: Antiviral protein SKI8Antiviral drug
    • RNA: RNA (5'-R(P*UP*UP*UP*U)-3')
KeywordsHelicase / RNA binding / RNA degradation / HYDROLASE
Function / homology
Function and homology information


Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / regulation of translation ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nuclear chromosome / mRNA catabolic process / regulation of translation / protein-containing complex assembly / defense response to virus / RNA helicase activity / RNA helicase / mRNA binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal ...Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Tetratricopeptide repeats / Tetratricopeptide repeat / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Tetratricopeptide-like helical domain superfamily / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Superkiller protein 3 / Antiviral helicase SKI2 / Antiviral protein SKI8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsKeidel A / Koegel A / Reichelt P / Kowalinski E / Schaefer IB / Conti E
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2023
Title: Concerted structural rearrangements enable RNA channeling into the cytoplasmic Ski238-Ski7-exosome assembly.
Authors: Achim Keidel / Alexander Kögel / Peter Reichelt / Eva Kowalinski / Ingmar B Schäfer / Elena Conti /
Abstract: The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the ...The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes.
History
DepositionAug 21, 2023-
Header (metadata) releaseNov 29, 2023-
Map releaseNov 29, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18288.png

Downloads & links

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Map

FileDownload / File: emd_18288.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8512 Å
Density
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.6680784 - 4.7996545
Average (Standard dev.)0.016025137 (±0.17343782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 245.1456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18288_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: local refined map of Ski2Arch Ski3N after signal subtraction...

Fileemd_18288_additional_1.map
Annotationlocal refined map of Ski2Arch_Ski3N after signal subtraction (cryoSPARC v3.3.2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: local refined map of Ski238-core after signal subtraction...

Fileemd_18288_additional_2.map
Annotationlocal refined map of Ski238-core after signal subtraction (cryoSPARC v3.3.2)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: map sharpened with deepEMhancer software (tightTarget)

Fileemd_18288_additional_3.map
Annotationmap sharpened with deepEMhancer software (tightTarget)
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_18288_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18288_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Ski238 polyU RNA

EntireName: Ski238 polyU RNA
Components
  • Complex: Ski238 polyU RNA
    • Protein or peptide: Antiviral helicase SKI2
    • Protein or peptide: Superkiller protein 3
    • Protein or peptide: Antiviral protein SKI8Antiviral drug
    • RNA: RNA (5'-R(P*UP*UP*UP*U)-3')

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Supramolecule #1: Ski238 polyU RNA

SupramoleculeName: Ski238 polyU RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3, #2, #4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Antiviral helicase SKI2

MacromoleculeName: Antiviral helicase SKI2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 146.259094 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSEGFSSSSI QELYQSLKEI TNNADVELFE DRITKLDFES TDEPKHANDI IKDRFLRPSN ALPWSLLDMV QDVPHTSSPE DCSGKLDYK ELLKVPDPIN RTSYQFKRTG LEGKISGYKE EVDLKEVANA NASNSLSITR SINHNQNSVR GSTAQLPFTP G GIPMKSVK ...String:
MSEGFSSSSI QELYQSLKEI TNNADVELFE DRITKLDFES TDEPKHANDI IKDRFLRPSN ALPWSLLDMV QDVPHTSSPE DCSGKLDYK ELLKVPDPIN RTSYQFKRTG LEGKISGYKE EVDLKEVANA NASNSLSITR SINHNQNSVR GSTAQLPFTP G GIPMKSVK TDSEQNGSST MANATKLLHK DGQGLFDIPE GMNRGIKPMD SPAENEDQNG QFKELKQLNE IDNELDIRIE AN EAKLKEE EKSAKSISEE IMEEATEETT ADNADDAEID ELLPIGIDFG RTKPVSKSVP VKKEWAHVVD LNHKIENFDE LIP NPARSW PFELDTFQKE AVYHLEQGDS VFVAAHTSAG KTVVAEYAIA MAHRNMTKTI YTSPIKALSN QKFRDFKETF DDVN IGLIT GDVQINPDAN CLIMTTEILR SMLYRGADLI RDVEFVIFDE VHYVNDQDRG VVWEEVIIML PQHVKFILLS ATVPN TYEF ANWIGRTKQK NIYVISTPKR PVPLEINIWA KKELIPVINQ NSEFLEANFR KHKEILNGES AKGAPSKTDN GRGGST ARG GRGGSNTRDG RGGRGNSTRG GANRGGSRGA GAIGSNKRKF FTQDGPSKKT WPEIVNYLRK RELLPMVVFV FSKKRCE EY ADWLEGINFC NNKEKSQIHM FIEKSITRLK KEDRDLPQIL KTRSLLERGI AVHHGGLLPI VKELIEILFS KGFIKVLF A TETFAMGLNL PTRTVIFSSI RKHDGNGLRE LTPGEFTQMA GRAGRRGLDS TGTVIVMAYN SPLSIATFKE VTMGVPTRL QSQFRLTYNM ILNLLRIEAL RVEEMIKYSF SENAKETLQP EHEKQIKVLQ EELQTIEYKS CEICDNDIEK FLELMLAYKE ATVNLMQEM VKSPSILHIL KEGRLVAFRD PNDCLKLGFV FKVSLKDAVC VIMTFTKPYK LPNGEPNHLI YFPKADGYRR R NFPKFQKT DFYMEEVPVT AIEVITKRKF AAPLGKVIKK DVAALNEFNA ETNNILDGKT LKEAINIEKQ GLKIHQILLD RT NIRDEIF KLKSIKCPNL SQHIVPKFKA HVIKKKIEEL YHLMSDQNLS LLPDYEKRLA VLKDTEFIDQ NHNVLLKGRV ACE INSGYE LVLTELILDN FLGSFEPEEI VALLSVFVYE GKTREEEPPI VTPRLAKGKQ RIEEIYKKML CVFNTHQIPL TQDE AEFLD RKRFAMMNVV YEWARGLSFK EIMEMSPEAE GTVVRVITWL DEICREVKTA SIIIGNSTLH MKMSRAQELI KRDIV FAAS LYL

UniProtKB: Antiviral helicase SKI2

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Macromolecule #2: Antiviral protein SKI8

MacromoleculeName: Antiviral protein SKI8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 44.283527 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSKVFIATAN AGKAHDADIF SVSACNSFTV SCSGDGYLKV WDNKLLDNEN PKDKSYSHFV HKSGLHHVDV LQAIERDAFE LCLVATTSF SGDLLFYRIT REDETKKVIF EKLDLLDSDM KKHSFWALKW GASNDRLLSH RLVATDVKGT TYIWKFHPFA D ESNSLTLN ...String:
MSKVFIATAN AGKAHDADIF SVSACNSFTV SCSGDGYLKV WDNKLLDNEN PKDKSYSHFV HKSGLHHVDV LQAIERDAFE LCLVATTSF SGDLLFYRIT REDETKKVIF EKLDLLDSDM KKHSFWALKW GASNDRLLSH RLVATDVKGT TYIWKFHPFA D ESNSLTLN WSPTLELQGT VESPMTPSQF ATSVDISERG LIATGFNNGT VQISELSTLR PLYNFESQHS MINNSNSIRS VK FSPQGSL LAIAHDSNSF GCITLYETEF GERIGSLSVP THSSQASLGE FAHSSWVMSL SFNDSGETLC SAGWDGKLRF WDV KTKERI TTLNMHCDDI EIEEDILAVD EHGDSLAEPG VFDVKFLKKG WRSGMGADLN ESLCCVCLDR SIRWFREAGG K

UniProtKB: Antiviral protein SKI8

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Macromolecule #3: Superkiller protein 3

MacromoleculeName: Superkiller protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 164.278484 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPDSMSDIKQ LLKEAKQELT NRDYEETIEI SEKVLKLDPD NYFAHIFLGK ALSSLPASNN VSSNRNLERA TNHYVSAAKL VPDNLLAWK GLFLLFRTTE VVPDILSYDE YFDLCGQYAD ALLKQEQSQV ELINDIKLLK KTHPDCQKAF YQHLKPGSLM A ETIGRHLS ...String:
GPDSMSDIKQ LLKEAKQELT NRDYEETIEI SEKVLKLDPD NYFAHIFLGK ALSSLPASNN VSSNRNLERA TNHYVSAAKL VPDNLLAWK GLFLLFRTTE VVPDILSYDE YFDLCGQYAD ALLKQEQSQV ELINDIKLLK KTHPDCQKAF YQHLKPGSLM A ETIGRHLS TPQDALLNLI KILSNIETTE IGKTLSQNRL KLKASDPDYQ IKLNSFSWEI IKNSEIDQLY NQLVNILADD QK RSEIENQ WLEYRIKVLK SMPLDVKKDF FTKVKEMVED MVLVNHQSLL AWQKYFEWTD YEDLDNMDAP LIIKYFKKFP KDP LAMILY SWLSSKLSKY DIKSLESANK PPEGHKKTEK ETDIKDVDET NEDEVKDRVE DEVKDRVEDE VKDQDEEAKE DEEE DLDDI EIGLLEEEVV TVLTENIVKC KNNILAHRIL CQYYLLTKEY EAALPYIKNG ISLIAYNIKD LGVHLPLTKR EFSLD LATV YTYVDAPKDH NAALKLYDNI LSGDFSNIQA KMGKGIIFIE RKNWKDAMTL LTQVHEQSPN NLEVLSELSW SKAHMG YMD EALAGLDTVI KGIKGMDLRS IDFRALNLWR QAKVYIMKHA SINDAKQENV KCAFKLLIQS IKILDTFAPG FSTLGDI YC HYYKDHLRAF KCYFKAFDLD AGDYTAAKYI TETYASKPNW QAASSIASRL IKGEKAKAEL RSNNWPFRVV GIAHLEKQ E ESDSIEWFQS ALRVDPNDVE SWVGLGQAYH ACGRIEASIK VFDKAIQLRP SHTFAQYFKA ISLCDVGEYL ESLDILEKV CQEAATEESF QIGLVEVLMR CSLDLYSQGF LLKSVSIAKD TIERIKIIIS ELKCENQQVW IYLSQVLRLF IWIESKVDTL PVESLVSIF ENSQFSGSEE IDSVDNIKID TLLDSTTDDN VSIACKFLIL ASKYSVSDQK FTDIAGTVRA SYWYNIGISE L TAFITLKE PQYRDAAIFA FKKSIQLQSN TSETWIGLGI ATMDINFRVS QHCFIKATAL EPKATNTWFN LAMLGLKKKD TE FAQQVLN KLQSLAPQDS SPWLGMALIL EEQGDIIGSS KLFAHSFILS NGRSKAAQFM YAKNVLENHI NNGDDERDIE TVE KLTTAS IALEQFFKKS PDSQFALQCA LLTLERLHHY ENANELANRL IGILEKKFEK TQDERELFNF AIIKGQFARI HLGL GNFEL SIENADLSQG IISESSDEKS MKTKISNHIC LGLSYFFLND FDQTLNQFQE LLSISKDSKH LVVLIAKVLY DVGES DTKE IALQELTEYI ATSGADLLVT LTIAAMSILD DKREDLSIIL EELKALPLSK QIIDKHKDAP YLIEEITKRL YRNDTG KQV WQRSAYFFPN NLKVWERLDK NIQRRIASNG QNKVTAEEMS KLYCESKNLR SIQRGMFLCP WNVTAVKALN ECF

UniProtKB: Superkiller protein 3

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Macromolecule #4: RNA (5'-R(P*UP*UP*UP*U)-3')

MacromoleculeName: RNA (5'-R(P*UP*UP*UP*U)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 9.140017 KDa
SequenceString:
UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU

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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: 7.4
GridModel: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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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: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 9416 / Average electron dose: 67.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 385414
FSC plot (resolution estimation)

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