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- EMDB-18328: CryoEM structure of a S. Cerevisiae Ski2387 complex in the open state -

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Basic information

Entry
Database: EMDB / ID: EMD-18328
TitleCryoEM structure of a S. Cerevisiae Ski2387 complex in the open state
Map dataMain map obtained from signal subtraction of Ski3-Nt followed by local refinement
Sample
  • Complex: Ski2delarch387 PolyU RNA
    • Protein or peptide: Antiviral helicase SKI2
    • Protein or peptide: Superkiller protein 3
    • Protein or peptide: Antiviral protein SKI8
    • Protein or peptide: Superkiller protein 7
KeywordsHelicase / RNA binding / RNA degradation / HYDROLASE
Function / homology
Function and homology information


mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / Ski complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nonfunctional rRNA decay / nuclear chromosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process ...mRNA decay by 3' to 5' exoribonuclease / protein-DNA complex assembly / Ski complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / reciprocal meiotic recombination / nonfunctional rRNA decay / nuclear chromosome / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / translational elongation / translation elongation factor activity / protein catabolic process / regulation of translation / protein-macromolecule adaptor activity / protein-containing complex assembly / defense response to virus / RNA helicase activity / RNA helicase / translation / GTPase activity / mRNA binding / protein-containing complex binding / GTP binding / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / : / Ski7 III domain / Ski7 domain II / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain ...Tetratricopeptide-like repeat / Tetratricopeptide repeat / : / : / Ski7 III domain / Ski7 domain II / : / Ski2, beta-barrel domain / Ski3/TTC37 / Ski2, N-terminal domain / Ski2 N-terminal region / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / : / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Tetratricopeptide repeat / Helicase conserved C-terminal domain / Tetratricopeptide-like helical domain superfamily / helicase superfamily c-terminal domain / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 / Superkiller protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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 25, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18328.png

Downloads & links

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Map

FileDownload / File: emd_18328.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map obtained from signal subtraction of Ski3-Nt followed by local refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 352 pix.
= 299.622 Å		0.85 Å/pix.
x 352 pix.
= 299.622 Å		0.85 Å/pix.
x 352 pix.
= 299.622 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-4.237769 - 5.681006
Average (Standard dev.)-0.0044864584 (±0.14757152)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 299.6224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18328_msk_1.map
Projections & Slices
AxesZYX

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Additional map: sharpened with deepEMhancer software (tightTarget)

Fileemd_18328_additional_1.map
Annotationsharpened with deepEMhancer software (tightTarget)
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: full map prior to signal subtraction

Fileemd_18328_additional_2.map
Annotationfull map prior to signal subtraction
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18328_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_18328_half_map_2.map
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Sample components

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Entire : Ski2delarch387 PolyU RNA

EntireName: Ski2delarch387 PolyU RNA
Components
  • Complex: Ski2delarch387 PolyU RNA
    • Protein or peptide: Antiviral helicase SKI2
    • Protein or peptide: Superkiller protein 3
    • Protein or peptide: Antiviral protein SKI8
    • Protein or peptide: Superkiller protein 7

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Supramolecule #1: Ski2delarch387 PolyU RNA

SupramoleculeName: Ski2delarch387 PolyU RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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 / EC number: RNA helicase
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: Superkiller protein 3

MacromoleculeName: Superkiller protein 3 / type: protein_or_peptide / ID: 2 / 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 #3: Antiviral protein SKI8

MacromoleculeName: Antiviral protein SKI8 / type: protein_or_peptide / ID: 3 / 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 #4: Superkiller protein 7

MacromoleculeName: Superkiller protein 7 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 28.345137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPDSMSLLEQ LARKRIEKSK GLLSADQSHS TSKSASLLER LHKNRETKDN NAETKRKDLK TLLAKDKVKR SDFTPNQHSV SLSLKLSAL KKSNSDLEKQ GKSVTLDSKE NELPTKRKSP DDKLNLEESW KAIKEMNHYC FLKNDPCINQ TDDFAFTNFI I KDKKNSLS ...String:
GPDSMSLLEQ LARKRIEKSK GLLSADQSHS TSKSASLLER LHKNRETKDN NAETKRKDLK TLLAKDKVKR SDFTPNQHSV SLSLKLSAL KKSNSDLEKQ GKSVTLDSKE NELPTKRKSP DDKLNLEESW KAIKEMNHYC FLKNDPCINQ TDDFAFTNFI I KDKKNSLS TSIPLSSQNS SFLSLKKHNN ELLGIFVPCN LPKTTRKVAI ENFNRPSPDD IIQSAQLNAF NEKLENLNIK SA GSWSHPQ FEK

UniProtKB: Superkiller protein 7

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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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 7127 / Average electron dose: 77.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 357690
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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