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- EMDB-51137: human SKI7-SKI238 complex in the open state -

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Basic information

Entry
Database: EMDB / ID: EMD-51137
Titlehuman SKI7-SKI238 complex in the open state
Map data
Sample
  • Complex: human SKI7-SKI238 complex in the open state
    • Protein or peptide: Superkiller complex protein 3
    • Protein or peptide: WD repeat-containing protein 61
    • Protein or peptide: Isoform 2 of HBS1-like protein
    • Protein or peptide: Superkiller complex protein 2
KeywordsHelicase / RNA-binding / RNA-degradation / cytoplasm / HYDROLASE
Function / homology
Function and homology information


Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / ribosome disassembly / Association of TriC/CCT with target proteins during biosynthesis ...Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / 3'-5' RNA helicase activity / ribosome disassembly / Association of TriC/CCT with target proteins during biosynthesis / nuclear-transcribed mRNA catabolic process / translation elongation factor activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / cytosolic ribosome / rescue of stalled ribosome / transcription elongation by RNA polymerase II / euchromatin / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / RNA helicase activity / RNA helicase / translation / GTPase activity / GTP binding / signal transduction / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
HBS1-like protein, N-terminal domain superfamily / Ski3/TTC37 / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal ...HBS1-like protein, N-terminal domain superfamily / Ski3/TTC37 / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / : / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / : / GTP-eEF1A C-terminal domain-like / : / Tetratricopeptide repeat / Tetratricopeptide repeat / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tetratricopeptide repeat / Translation elongation factor EFTu-like, domain 2 / TPR repeat region circular profile. / Elongation factor Tu domain 2 / TPR repeat profile. / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Tetratricopeptide repeats / 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 / Translation protein, beta-barrel domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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 complex protein 2 / Superkiller complex protein 3 / Superkiller complex protein 8 / HBS1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKoegel A / Keidel A / Loukeri MJ / Kuhn CC / Langer LM / Schaefer IB / Conti E
Funding support Germany, European Union, Denmark, 5 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Research Council (ERC)740329European Union
European Research Council (ERC)101054447European Union
German Research Foundation (DFG)SFB1035 Germany
Novo Nordisk Foundation31199 Denmark
CitationJournal: Nature / Year: 2024
Title: Structural basis of mRNA decay by the human exosome-ribosome supercomplex.
Authors: Alexander Kögel / Achim Keidel / Matina-Jasemi Loukeri / Christopher C Kuhn / Lukas M Langer / Ingmar B Schäfer / Elena Conti /
Abstract: The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated ...The interplay between translation and mRNA decay is widespread in human cells. In quality-control pathways, exonucleolytic degradation of mRNA associated with translating ribosomes is mediated largely by the cytoplasmic exosome, which includes the exoribonuclease complex EXO10 and the helicase complex SKI238 (refs. ). The helicase can extract mRNA from the ribosome and is expected to transfer it to the exoribonuclease core through a bridging factor, HBS1L3 (also known as SKI7), but the mechanisms of this molecular handover remain unclear. Here we reveal how human EXO10 is recruited by HBS1L3 (SKI7) to an active ribosome-bound SKI238 complex. We show that rather than a sequential handover, a direct physical coupling mechanism takes place, which culminates in the formation of a cytoplasmic exosome-ribosome supercomplex. Capturing the structure during active decay reveals a continuous path in which an RNA substrate threads from the 80S ribosome through the SKI2 helicase into the exoribonuclease active site of the cytoplasmic exosome complex. The SKI3 subunit of the complex directly binds to HBS1L3 (SKI7) and also engages a surface of the 40S subunit, establishing a recognition platform in collided disomes. Exosome and ribosome thus work together as a single structural and functional unit in co-translational mRNA decay, coordinating their activities in a transient supercomplex.
History
DepositionJul 23, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51137.png

Downloads & links

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Map

FileDownload / File: emd_51137.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å		0.85 Å/pix.
x 832 pix.
= 708.198 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.039971717 - 0.09765662
Average (Standard dev.)0.000011183273 (±0.0006685534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions832832832
Spacing832832832
CellA=B=C: 708.19836 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51137_msk_1.map
Projections & Slices
AxesZYX

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Half map: half2

Fileemd_51137_half_map_1.map
Annotationhalf2
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half1

Fileemd_51137_half_map_2.map
Annotationhalf1
Projections & Slices
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Sample components

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Entire : human SKI7-SKI238 complex in the open state

EntireName: human SKI7-SKI238 complex in the open state
Components
  • Complex: human SKI7-SKI238 complex in the open state
    • Protein or peptide: Superkiller complex protein 3
    • Protein or peptide: WD repeat-containing protein 61
    • Protein or peptide: Isoform 2 of HBS1-like protein
    • Protein or peptide: Superkiller complex protein 2

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Supramolecule #1: human SKI7-SKI238 complex in the open state

SupramoleculeName: human SKI7-SKI238 complex in the open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Superkiller complex protein 3

MacromoleculeName: Superkiller complex protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 176.06475 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPDSMSSKEV KTALKSARDA IRNKEYKEAL KHCKTVLKQE KNNYNAWVFI GVAAAELEQP DQAQSAYKKA AELEPDQLLA WQGLANLYE KYNHINAKDD LPGVYQKLLD LYESVDKQKW CDVCKKLVDL YYQEKKHLEV ARTWHKLIKT RQEQGAENEE L HQLWRKLT ...String:
GPDSMSSKEV KTALKSARDA IRNKEYKEAL KHCKTVLKQE KNNYNAWVFI GVAAAELEQP DQAQSAYKKA AELEPDQLLA WQGLANLYE KYNHINAKDD LPGVYQKLLD LYESVDKQKW CDVCKKLVDL YYQEKKHLEV ARTWHKLIKT RQEQGAENEE L HQLWRKLT QFLAESTEDQ NNETQQLLFT AFENALGLSD KIPSEDHQVL YRHFIQSLSK FPHESARLKK ACEGMINIYP TV QYPLEVL CLHLIESGNL TDEGQQYCCR LVEMDSKSGP GLIGLGIKAL QDKKYEDAVR NLTEGLKESP VCTSGWYHLA EAQ VKMHRP KEAVLSCSQA LKIVDNLGAS GNSLYQRNLC LHLKAEALIK LSDYDSSEEA IRTLDQISDA DNIPGLLVLK SLAY RNKGS FDEAAKIMED LLSSYPDLAE VHALEALIHF TKKDYLQAEK CFQRALEKDT EVAEYHYQLG LTYWFMGEET RKDKT KALT HFLKAARLDT YMGKVFCYLG HYYRDVVGDK NRARGCYRKA FELDDTDAES GAAAVDLSVE LEDMEMALAI LTTVTQ KAS AGTAKWAWLR RGLYYLKAGQ HSQAVADLQA ALRADPKDFN CWESLGEAYL SRGGYTTALK SFTKASELNP ESIYSVF KV AAIQQILGKY KEAVAQYQMI IKKKEDYVPA LKGLGECHLM MAKAALVDYL DGKAVDYIEK ALEYFTCALQ HRADVSCL W KLAGDACTCL YAVAPSKVNV HVLGVLLGQK EGKQVLKKNE LLHLGGRCYG RALKLMSTSN TWCDLGINYY RQAQHLAET GSNMNDLKEL LEKSLHCLKK AVRLDSNNHL YWNALGVVAC YSGIGNYALA QHCFIKSIQS EQINAVAWTN LGVLYLTNEN IEQAHEAFK MAQSLDPSYL MCWIGQALIA EAVGSYDTMD LFRHTTELNM HTEGALGYAY WVCTTLQDKS NRETELYQYN I LQMNAIPA AQVILNKYVE RIQNYAPAFT MLGYLNEHLQ LKKEAANAYQ RAILLLQTAE DQDTYNVAIR NYGRLLCSTG EY DKAIQAF KSTPLEVLED IIGFALALFM KGLYKESSKA YERALSIVES EQDKAHILTA LAITEYKQGK TDVAKTLLFK CSI LKEPTT ESLQALCALG LAMQDATLSK AALNELLKHI KHKDSNYQRC LLTSAIYALQ GRSVAVQKQI SKAVHSNPGD PALW SLLSR VVAQYAQRNA KGGVVAGNVA HILDSNHGKK ALLYTAVNQL AMGSSSAEDE KNTALKTIQK AALLSPGDPA IWAGL MAAC HADDKLALVN NTQPKRIDLY LALLSAVSAS IKDEKFFENY NQSLEKWSLS QAVTGLIDTG RISEAETLCT KNLKSN PDQ PAVILLLRQV QCKPLLESQK PLPDAVLEEL QKTVMSNSTS VPAWQWLAHV YQSQGMMRAA EMCYRKSLQL ASQRGSW SG KLSSLLRLAL LALKVCMANI SNDHWPSLVQ EATTEALKLC FCPLAVLLQA LLQFKRKMGA RETRRLLERV VYQPGYPK S IASTARWYLL RHLYAKDDYE LIDVLVNNAK THGDTRALEL NQRLSSQ

UniProtKB: Superkiller complex protein 3

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Macromolecule #2: WD repeat-containing protein 61

MacromoleculeName: WD repeat-containing protein 61 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.617465 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI ...String:
MTNQYGILFK QEQAHDDAIW SVAWGTNKKE NSETVVTGSL DDLVKVWKWR DERLDLQWSL EGHQLGVVSV DISHTLPIAA SSSLDAHIR LWDLENGKQI KSIDAGPVDA WTLAFSPDSQ YLATGTHVGK VNIFGVESGK KEYSLDTRGK FILSIAYSPD G KYLASGAI DGIINIFDIA TGKLLHTLEG HAMPIRSLTF SPDSQLLVTA SDDGYIKIYD VQHANLAGTL SGHASWVLNV AF CPDDTHF VSSSSDKSVK VWDVGTRTCV HTFFDHQDQV WGVKYNGNGS KIVSVGDDQE IHIYDCPI

UniProtKB: Superkiller complex protein 8

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Macromolecule #3: Isoform 2 of HBS1-like protein

MacromoleculeName: Isoform 2 of HBS1-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.333492 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPDSESPSLT ELFQEHKENN ISQCFTLSDL CNQSSASFTD LSLGSFPLSQ LANRCQSSPG ISELTGSLSS LAFHKASPTR DLENLSLSE LIAETIDVDN SQIKKESFEV SLSEVRSPGI DSNIDLSVLI KNPDFVPKPV VDPSIAPSSR TKVLSSKLGK N SNFAKDNK KNNKGSLTRK P

UniProtKB: HBS1-like protein

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Macromolecule #4: Superkiller complex protein 2

MacromoleculeName: Superkiller complex protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.617375 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN ...String:
MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ LFLSSPAWLP LHGVEHSARK WQRKTDPWS LLAVLGAPVP SDLQAQRHPT TGQILGYKEV LLENTNLSAT TSLSLRRPPG PASQSLWGNP TQYPFWPGGM D EPTITDLN TREEAEEEID FEKDLLTIPP GFKKGMDFAP KDCPTPAPGL LSLSCMLEPL DLGGGDEDEN EAVGQPGGPR GD TVSASPC SAPLARASSL EDLVLKEAST AVSTPEAPEP PSQEQWAIPV DATSPVGDFY RLIPQPAFQW AFEPDVFQKQ AIL HLERHD SVFVAAHTSA GKTVVAEYAI ALAQKHMTRT IYTSPIKALS NQKFRDFRNT FGDVGLLTGD VQLHPEASCL IMTT EILRS MLYSGSDVIR DLEWVIFDEV HYINDVERGV VWEEVLIMLP DHVSIILLSA TVPNALEFAD WIGRLKRRQI YVIST VTRP VPLEHYLFTG NSSKTQGELF LLLDSRGAFH TKGYYAAVEA KKERMSKHAQ TFGAKQPTHQ GGPAQDRGVY LSLLAS LRT RAQLPVVVFT FSRGRCDEQA SGLTSLDLTT SSEKSEIHLF LQRCLARLRG SDRQLPQVLH MSELLNRGLG VHHSGIL PI LKEIVEMLFS RGLVKVLFAT ETFAMGVNMP ARTVVFDSMR KHDGSTFRDL LPGEYVQMAG RAGRRGLDPT GTVILLCK G RVPEMADLHR MMMGKPSQLQ SQFRLTYTMI LNLLRVDALR VEDMMKRSFS EFPGSRGLLL LPEYHQRVEV LRTLGYVDE AGTVKLAGRV ACAMSSHELL LTELMFDNAL STLRPEEIAA LLSGLVCQSP GDAGDQLPNT LKQGIERVRA VAKRIGEVQV ACGLNQTVE EFVGELNFGL VEVVYEWARG MPFSELAGLS GTPEGLVVRC IQRLAEMCRS LRGAARLVGE PVLGAKMETA A TLLRRDIV FAASLYTQ

UniProtKB: Superkiller complex protein 2, Superkiller complex protein 2

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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: 7.5
GridModel: Quantifoil R2/1 / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 67.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7qds

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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