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- PDB-9g8o: human 40S ribosome bound by a SKI238-exosome complex -

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Basic information

Entry
Database: PDB / ID: 9g8o
Titlehuman 40S ribosome bound by a SKI238-exosome complex
Components
  • (40S ribosomal protein ...) x 31
  • (Exosome complex component ...) x 9
  • 18S ribosomal RNA
  • 60S ribosomal protein L41
  • CrPV-IRES RNA
  • DIS3-like exonuclease 1
  • Helicase SKI2W
  • Isoform 2 of HBS1-like protein
  • Receptor of activated protein C kinase 1
  • Superkiller complex protein 3
  • Ubiquitin
  • WD repeat-containing protein 61
KeywordsRIBOSOME / RNA-binding / RNA-degradation / cytoplasm / helicase
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II / exoribonuclease II activity / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / CUT catabolic process / U1 snRNA 3'-end processing / Ski complex / U5 snRNA 3'-end processing ...DNA deamination / nucleolar exosome (RNase complex) / exoribonuclease II / exoribonuclease II activity / Dom34-Hbs1 complex / nuclear-transcribed mRNA catabolic process, no-go decay / CUT catabolic process / U1 snRNA 3'-end processing / Ski complex / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / exosome (RNase complex) / cytoplasmic exosome (RNase complex) / mRNA decay by 3' to 5' exoribonuclease / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / Cdc73/Paf1 complex / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of myeloid cell differentiation / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / histone mRNA catabolic process / positive regulation of isotype switching / 3'-5' RNA helicase activity / nuclear mRNA surveillance / rRNA catabolic process / Nuclear RNA decay / 7S RNA binding / isotype switching / mRNA 3'-UTR AU-rich region binding / negative regulation of endoplasmic reticulum unfolded protein response / ribosome disassembly / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / RNA catabolic process / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of DNA-templated transcription initiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of RNA splicing / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / neural crest cell differentiation / supercoiled DNA binding / cytoplasmic translational initiation / NF-kappaB complex / negative regulation of DNA repair / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / nuclear chromosome / ion channel inhibitor activity / mRNA catabolic process / protein kinase A binding / laminin receptor activity / Ribosomal scanning and start codon recognition / pigmentation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of mitochondrial depolarization / Translation initiation complex formation / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / SARS-CoV-1 modulates host translation machinery / positive regulation of GTPase activity / mTORC1-mediated signalling / TOR signaling / iron-sulfur cluster binding / Peptide chain elongation / regulation of cell division / nuclear-transcribed mRNA catabolic process / cellular response to ethanol / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of protein binding
Similarity search - Function
Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / Ski3/TTC37 / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain ...Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / Ski3/TTC37 / HBS1-like protein, N-terminal domain superfamily / HBS1-like protein, N-terminal / HBS1 N-terminus / Ski2, N-terminal domain / Ski2 N-terminal region / Exosome complex exonuclease RRP44, S1 domain / S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / : / rRNA-processing arch domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Mtr4-like, beta-barrel domain / : / : / Ribonuclease II/R / RNB domain / RNB / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / : / GTP-eEF1A C-terminal domain-like / : / Tetratricopeptide repeat / K Homology domain, type 1 / Tetratricopeptide repeat / K Homology domain, type 1 superfamily / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Tetratricopeptide repeat / Ubiquitin-like protein FUBI / : / Ribosomal protein S26e signature. / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / : / Ribosomal protein S12e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein S12e / TPR repeat region circular profile. / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / Elongation factor Tu domain 2 / 40S Ribosomal protein S10 / S27a-like superfamily / Plectin/S10, N-terminal / Plectin/S10 domain / TPR repeat profile. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S25 / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / :
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Superkiller complex protein 2 / Exosome complex component MTR3 / Superkiller complex protein 3 / DIS3-like exonuclease 1 / Exosome complex component RRP43 / Superkiller complex protein 8 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex component CSL4 / HBS1-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Cricket paralysis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKoegel, A. / Keidel, A. / Loukeri, M.J. / Kuhn, C.C. / Langer, L.M. / Schaefer, I.B. / Conti, E.
Funding support Germany, European Union, Denmark, 5items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _em_admin.last_update
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Superkiller complex protein 3
C: WD repeat-containing protein 61
D: WD repeat-containing protein 61
F: Exosome complex component RRP42
J: Exosome complex component CSL4
K: Exosome complex component RRP45
L: Exosome complex component RRP43
N: Exosome complex component RRP41
O: Exosome complex component RRP46
A: Helicase SKI2W
E: Isoform 2 of HBS1-like protein
G: Exosome complex component MTR3
H: Exosome complex component RRP40
I: Exosome complex component RRP4
X: CrPV-IRES RNA
Ln: 60S ribosomal protein L41
M: DIS3-like exonuclease 1
S2: 18S ribosomal RNA
SA: 40S ribosomal protein SA
SB: 40S ribosomal protein S3a
SC: 40S ribosomal protein S2
SD: 40S ribosomal protein S3
SE: 40S ribosomal protein S4, X isoform
SF: 40S ribosomal protein S5
SG: 40S ribosomal protein S6
SH: 40S ribosomal protein S7
SI: 40S ribosomal protein S8
SJ: 40S ribosomal protein S9
SK: 40S ribosomal protein S10
SL: 40S ribosomal protein S11
SM: 40S ribosomal protein S12
SN: 40S ribosomal protein S13
SO: 40S ribosomal protein S14
SP: 40S ribosomal protein S15
SQ: 40S ribosomal protein S16
SR: 40S ribosomal protein S17
SS: 40S ribosomal protein S18
ST: 40S ribosomal protein S19
SU: 40S ribosomal protein S20
SV: 40S ribosomal protein S21
SW: 40S ribosomal protein S15a
SX: 40S ribosomal protein S23
SY: 40S ribosomal protein S24
SZ: 40S ribosomal protein S25
Sa: 40S ribosomal protein S26
Sb: 40S ribosomal protein S27
Sc: 40S ribosomal protein S28
Sd: 40S ribosomal protein S29
Se: 40S ribosomal protein S30
Sf: Ubiquitin
Sg: Receptor of activated protein C kinase 1


Theoretical massNumber of molelcules
Total (without water)2,118,72151
Polymers2,118,72151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 7 types, 8 molecules BCDAEMSfSg

#1: Protein Superkiller complex protein 3 / Ski3 / Tetratricopeptide repeat protein 37 / TPR repeat protein 37 / Tricho-hepatic-enteric ...Ski3 / Tetratricopeptide repeat protein 37 / TPR repeat protein 37 / Tricho-hepatic-enteric syndrome protein / Thespin


Mass: 176064.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIC3, KIAA0372, TTC37 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6PGP7
#2: Protein WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog / SKI8 homolog / Ski8


Mass: 33617.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GZS3
#9: Protein Helicase SKI2W / Ski2 / Helicase-like protein / HLP


Mass: 137913.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKIV2L, DDX13, SKI2W, SKIV2, W / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q15477, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#10: Protein Isoform 2 of HBS1-like protein / ERFS


Mass: 30196.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBS1L, HBS1, KIAA1038 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y450, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#16: Protein DIS3-like exonuclease 1


Mass: 125229.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIS3L, DIS3L1, KIAA1955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TF46, exoribonuclease II
#49: Protein Ubiquitin


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#50: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244

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Exosome complex component ... , 9 types, 9 molecules FJKLNOGHI

#3: Protein Exosome complex component RRP42 / Exosome component 7 / Ribosomal RNA-processing protein 42 / p8


Mass: 32216.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC7, KIAA0116, RRP42 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15024
#4: Protein Exosome complex component CSL4 / Exosome component 1


Mass: 21835.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC1, CSL4, CGI-108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B2
#5: Protein Exosome complex component RRP45 / Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome- ...Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome-associated autoantigen / Polymyositis/scleroderma autoantigen 1 / Polymyositis/scleroderma autoantigen 75 kDa / PM/Scl-75


Mass: 49370.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC9, PMSCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06265
#6: Protein Exosome complex component RRP43 / Exosome component 8 / Opa-interacting protein 2 / OIP-2 / Ribosomal RNA-processing protein 43 / p9


Mass: 30429.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC8, OIP2, RRP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B26
#7: Protein Exosome complex component RRP41 / Exosome component 4 / Ribosomal RNA-processing protein 41 / p12A


Mass: 26416.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC4, RRP41, SKI6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPD3
#8: Protein Exosome complex component RRP46 / Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing ...Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing protein 46 / p12B


Mass: 25636.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC5, CML28, RRP46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT4
#11: Protein Exosome complex component MTR3 / Exosome component 6 / mRNA transport regulator 3 homolog / hMtr3 / p11


Mass: 28267.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC6, MTR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RKV6
#12: Protein Exosome complex component RRP40 / Exosome component 3 / Ribosomal RNA-processing protein 40 / p10


Mass: 29940.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC3, RRP40, CGI-102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT5
#13: Protein Exosome complex component RRP4 / Exosome component 2 / Ribosomal RNA-processing protein 4


Mass: 33190.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC2, RRP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13868

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RNA chain , 2 types, 2 molecules XS2

#14: RNA chain CrPV-IRES RNA


Mass: 79333.953 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Cricket paralysis virus
#17: RNA chain 18S ribosomal RNA


Mass: 602752.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Protein/peptide , 1 types, 1 molecules Ln

#15: Protein/peptide 60S ribosomal protein L41 / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

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40S ribosomal protein ... , 31 types, 31 molecules SASBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSUSVSWSXSYSZSaSbScSdSe

#18: Protein 40S ribosomal protein SA / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#19: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#20: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#21: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#22: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#23: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#24: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#25: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#26: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#27: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#28: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#29: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#30: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 14548.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#31: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#32: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#33: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#34: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#35: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#36: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#37: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#38: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866
#39: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#40: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#41: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#42: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#43: Protein 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#44: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#45: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#46: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#47: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#48: Protein 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human 40S ribosome bound by a SKI238-exosome complex / Type: RIBOSOME
Entity ID: #14, #34-#39, #41, #44, #46, #15, #47, #49-#50, #20, #24, #17, #27, #30, #18, #31, #19, #32, #21, #40, #22, #42, #9, #1-#2, #23, #43, #3, #11-#13, #4-#5, #10, #16, #6-#8, #25, #45, #26, #48, #28-#29, #33
Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 64.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53460 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005131359
ELECTRON MICROSCOPYf_angle_d0.735186304
ELECTRON MICROSCOPYf_dihedral_angle_d15.91855530
ELECTRON MICROSCOPYf_chiral_restr0.04722475
ELECTRON MICROSCOPYf_plane_restr0.00516952

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