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- EMDB-14515: Human NEXT dimer in complex with the nuclear RNA exosome -

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Basic information

Entry
Database: EMDB / ID: EMD-14515
TitleHuman NEXT dimer in complex with the nuclear RNA exosome
Map dataNEXT_S_with_nuclear_exosome_refine
Sample
  • Complex: Human NEXT dimer in complex with the nuclear RNA exosome
    • Complex: Human NEXT dimer in complex with the nuclear RNA exosome
      • Protein or peptide: x 15 types
    • Complex: RNA 5 prime hairpin U60
      • RNA: x 1 types
KeywordsHELICASE / ATPASE / RNA DEGRADATION / EXOSOME / RNA BINDING PROTEIN
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / : / snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome ...DNA deamination / nucleolar exosome (RNase complex) / : / snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / U1 snRNA 3'-end processing / positive regulation of mRNA cis splicing, via spliceosome / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / regulation of telomerase RNA localization to Cajal body / nuclear polyadenylation-dependent rRNA catabolic process / RNA exonuclease activity / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / 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 / snRNA binding / ATF4 activates genes in response to endoplasmic reticulum stress / rRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / positive regulation of isotype switching / histone mRNA catabolic process / nuclear mRNA surveillance / mRNA 3'-UTR AU-rich region binding / 7S RNA binding / isotype switching / telomerase RNA binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of alternative mRNA splicing, via spliceosome / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / negative regulation of telomere maintenance via telomerase / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / pre-mRNA intronic binding / catalytic step 2 spliceosome / transcription repressor complex / mRNA Splicing - Major Pathway / small-subunit processome / guanyl-nucleotide exchange factor activity / 14-3-3 protein binding / meiotic cell cycle / nuclear receptor binding / euchromatin / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / rRNA processing / transcription corepressor activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / positive regulation of cell growth / defense response to virus / endonuclease activity / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / single-stranded RNA binding / nuclear body / RNA helicase / nuclear speck / immune response / nucleotide binding / DNA repair / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / DNA-templated transcription / apoptotic process / DNA damage response / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mammalian exosome complex component RRP40, N-terminal / RBM7, RNA recognition motif / Exosome-associated factor Rrp47/DNA strand repair C1D / M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 ...: / Mammalian exosome complex component RRP40, N-terminal / RBM7, RNA recognition motif / Exosome-associated factor Rrp47/DNA strand repair C1D / M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / : / Exosome complex component RRP40, S1 domain / Exosome-associated factor Rrp6, N-terminal / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome complex exonuclease Rrp6-like / PMC2NT (NUC016) domain / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / PIN domain / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / : / Exosome RNA helicase MTR4-like, stalk / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / DSHCT (NUC185) domain / DSHCT / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / 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 / PSP, proline-rich / PSP / proline-rich domain in spliceosome associated proteins / HRDC domain superfamily / 3'-5' exonuclease / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / 3'-5' exonuclease / 3'-5' exonuclease domain / K Homology domain, type 1 superfamily / PIN-like domain superfamily / HRDC-like superfamily / Ribosomal protein S1-like RNA-binding domain / S1 domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Helicase conserved C-terminal domain / RNA-binding domain superfamily / zinc finger / Zinc knuckle / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Exosome RNA helicase MTR4 / Exosome complex component 10 / Exosome complex component RRP45 / Exosome complex component RRP4 / Nuclear nucleic acid-binding protein C1D / Exosome complex component RRP42 / Exosome complex component MTR3 / Zinc finger CCHC domain-containing protein 8 / M-phase phosphoprotein 6 / Exosome complex component RRP41 ...Exosome RNA helicase MTR4 / Exosome complex component 10 / Exosome complex component RRP45 / Exosome complex component RRP4 / Nuclear nucleic acid-binding protein C1D / Exosome complex component RRP42 / Exosome complex component MTR3 / Zinc finger CCHC domain-containing protein 8 / M-phase phosphoprotein 6 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex exonuclease RRP44 / Exosome complex component CSL4 / RNA-binding protein 7
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsGerlach P / Lingaraju M / Salerno-Kochan A / Bonneau F / Basquin J / Conti E
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
Max Planck Society Germany
European CommissionERC-2016-ADG 740329 EXORICOEuropean Union
German Research Foundation (DFG)SFB/TRR 237 Germany
German Research Foundation (DFG)SFB 1035 Germany
CitationJournal: Mol Cell / Year: 2022
Title: Structure and regulation of the nuclear exosome targeting complex guides RNA substrates to the exosome.
Authors: Piotr Gerlach / William Garland / Mahesh Lingaraju / Anna Salerno-Kochan / Fabien Bonneau / Jérôme Basquin / Torben Heick Jensen / Elena Conti /
Abstract: In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting ...In mammalian cells, spurious transcription results in a vast repertoire of unproductive non-coding RNAs, whose deleterious accumulation is prevented by rapid decay. The nuclear exosome targeting (NEXT) complex plays a central role in directing non-functional transcripts to exosome-mediated degradation, but the structural and molecular mechanisms remain enigmatic. Here, we elucidated the architecture of the human NEXT complex, showing that it exists as a dimer of MTR4-ZCCHC8-RBM7 heterotrimers. Dimerization preconfigures the major MTR4-binding region of ZCCHC8 and arranges the two MTR4 helicases opposite to each other, with each protomer able to function on many types of RNAs. In the inactive state of the complex, the 3' end of an RNA substrate is enclosed in the MTR4 helicase channel by a ZCCHC8 C-terminal gatekeeping domain. The architecture of a NEXT-exosome assembly points to the molecular and regulatory mechanisms with which the NEXT complex guides RNA substrates to the exosome.
History
DepositionMar 7, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14515.png

Downloads & links

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Map

FileDownload / File: emd_14515.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNEXT_S_with_nuclear_exosome_refine
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å		1.35 Å/pix.
x 400 pix.
= 540. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
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Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.0233095 - 0.039567996
Average (Standard dev.)-0.00000018423991 (±0.0015498896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 540.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14515_msk_1.map
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Additional map: NEXT S with nuclear exosome refine low pass 10

Fileemd_14515_additional_1.map
AnnotationNEXT_S_with_nuclear_exosome_refine_low_pass_10
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Additional map: NEXT S with nuclear exosome 3Dclass

Fileemd_14515_additional_2.map
AnnotationNEXT_S_with_nuclear_exosome_3Dclass
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Half map: NEXT S with nuclear exosome half map 1

Fileemd_14515_half_map_1.map
AnnotationNEXT_S_with_nuclear_exosome_half_map_1
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Half map: NEXT S with nuclear exosome half map 2

Fileemd_14515_half_map_2.map
AnnotationNEXT_S_with_nuclear_exosome_half_map_2
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Sample components

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Entire : Human NEXT dimer in complex with the nuclear RNA exosome

EntireName: Human NEXT dimer in complex with the nuclear RNA exosome
Components
  • Complex: Human NEXT dimer in complex with the nuclear RNA exosome
    • Complex: Human NEXT dimer in complex with the nuclear RNA exosome
      • Protein or peptide: Exosome RNA helicase MTR4
      • Protein or peptide: Zinc finger CCHC domain-containing protein 8
      • Protein or peptide: RNA-binding protein 7
      • Protein or peptide: M-phase phosphoprotein 6
      • Protein or peptide: Nuclear nucleic acid-binding protein C1D
      • Protein or peptide: Exosome component 10
      • Protein or peptide: Exosome complex component CSL4
      • Protein or peptide: Exosome complex component RRP4
      • Protein or peptide: Exosome complex component RRP40
      • Protein or peptide: Exosome complex component RRP41
      • Protein or peptide: Exosome complex component RRP46
      • Protein or peptide: Exosome complex component MTR3
      • Protein or peptide: Exosome complex component RRP42
      • Protein or peptide: Exosome complex component RRP45
      • Protein or peptide: Exosome complex exonuclease RRP44
    • Complex: RNA 5 prime hairpin U60
      • RNA: RNA 5 prime hairpin U60

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Supramolecule #1: Human NEXT dimer in complex with the nuclear RNA exosome

SupramoleculeName: Human NEXT dimer in complex with the nuclear RNA exosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Human NEXT dimer in complex with the nuclear RNA exosome

SupramoleculeName: Human NEXT dimer in complex with the nuclear RNA exosome
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#15
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: RNA 5 prime hairpin U60

SupramoleculeName: RNA 5 prime hairpin U60 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #16
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADAFGDELF SVFEGDSTTA AGTKKDKEKD KGKWKGPPGS ADKAGKRFDG KLQSESTNNG KNKRDVDFE GTDEPIFGKK PRIEESITED LSLADLMPRV KVQSVETVEG CTHEVALPAE E DYLPLKPR VGKAAKEYPF ILDAFQREAI QCVDNNQSVL VSAHTSAGKT ...String:
MADAFGDELF SVFEGDSTTA AGTKKDKEKD KGKWKGPPGS ADKAGKRFDG KLQSESTNNG KNKRDVDFE GTDEPIFGKK PRIEESITED LSLADLMPRV KVQSVETVEG CTHEVALPAE E DYLPLKPR VGKAAKEYPF ILDAFQREAI QCVDNNQSVL VSAHTSAGKT VCAEYAIALA LR EKQRVIF TSPIKALSNQ KYREMYEEFQ DVGLMTGDVT INPTASCLVM TTEILRSMLY RGS EVMREV AWVIFDEIHY MRDSERGVVW EETIILLPDN VHYVFLSATI PNARQFAEWI CHLH KQPCH VIYTDYRPTP LQHYIFPAGG DGLHLVVDEN GDFREDNFNT AMQVLRDAGD LAKGD QKGR KGGTKGPSNV FKIVKMIMER NFQPVIIFSF SKKDCEAYAL QMTKLDFNTD EEKKMV EEV FSNAIDCLSD EDKKLPQVEH VLPLLKRGIG IHHGGLLPIL KETIEILFSE GLIKALF AT ETFAMGINMP ARTVLFTNAR KFDGKDFRWI SSGEYIQMSG RAGRRGMDDR GIVILMVD E KMSPTIGKQL LKGSADPLNS AFHLTYNMVL NLLRVEEINP EYMLEKSFYQ FQHYRAIPG VVEKVKNSEE QYNKIVIPNE ESVVIYYKIR QQLAKLGKEI EEYIHKPKYC LPFLQPGRLV KVKNEGDDF GWGVVVNFSK KSNVKPNSGE LDPLYVVEVL LRCSKESLKN SATEAAKPAK P DEKGEMQV VPVLVHLLSA ISSVRLYIPK DLRPVDNRQS VLKSIQEVQK RFPDGIPLLD PI DDMGIQD QGLKKVIQKV EAFEHRMYSH PLHNDPNLET VYTLCEKKAQ IAIDIKSAKR ELK KARTVL QMDELKCRKR VLRRLGFATS SDVIEMKGRV ACEISSADEL LLTEMMFNGL FNDL SAEQA TALLSCFVFQ ENSSEMPKLT EQLAGPLRQM QECAKRIAKV SAEAKLEIDE ETYLS SFKP HLMDVVYTWA TGATFAHICK MTDVFEGSII RCMRRLEELL RQMCQAAKAI GNTELE NKF AEGITKIKRD IVFAASLYL

UniProtKB: Exosome RNA helicase MTR4

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Macromolecule #2: Zinc finger CCHC domain-containing protein 8

MacromoleculeName: Zinc finger CCHC domain-containing protein 8 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ENGVGDAELR ERLRQCEET IEQLRAENQE LKRKLNILTR PSGILVNDTK LDGPILQILF M NNAISKQY HQEIEEFVSN LVKRFEEQQK NDVEKTSFNL LPQPSSIVLE ED HKVEESC AIKNNKEAFS VVGSVLYFTN FCLDKLGQPL LNENPQLSEG WEI PKYHQV ...String:
ENGVGDAELR ERLRQCEET IEQLRAENQE LKRKLNILTR PSGILVNDTK LDGPILQILF M NNAISKQY HQEIEEFVSN LVKRFEEQQK NDVEKTSFNL LPQPSSIVLE ED HKVEESC AIKNNKEAFS VVGSVLYFTN FCLDKLGQPL LNENPQLSEG WEI PKYHQV FSHIVSLEGQ EIQVKAKRPK PHCFNCGSEE HQMKDCPMPR NAAR ISEKR KEYMDACGEA NNQNFQQRYH AEEVEERFGR FKPGVISEEL QDALG VTDK SLPPFIYRMR QLGYPPGWLK EAELENSGLA LYD

UniProtKB: Zinc finger CCHC domain-containing protein 8

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Macromolecule #3: RNA-binding protein 7

MacromoleculeName: RNA-binding protein 7 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MGAAAAEADR TLFVGNLETK VTEELLFELF HQAGPVIKVK IPKDKDGKPK QFAFVNFKH EVSVPYAMNL LNGIKLYGRP IKIQFRSGSS HAPQDVSLS

UniProtKB: RNA-binding protein 7

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Macromolecule #4: M-phase phosphoprotein 6

MacromoleculeName: M-phase phosphoprotein 6 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAAERKTRLS KNLLRMKFMQ RGLDSETKKQ LEEEEKKIIS EEHWYLDLPE LKEKESFIIE EQSFLLCEDL LYGRMSFRGF NPEVEKLMLQ MNAKHKAEEV EDETVELDVS DEEMARRYET LVGTIGKKFA RKRDHANYEE DENGDITPIK AKKMFLKPQD

UniProtKB: M-phase phosphoprotein 6

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Macromolecule #5: Nuclear nucleic acid-binding protein C1D

MacromoleculeName: Nuclear nucleic acid-binding protein C1D / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAGEEINEDY PVEIHEYLSA FENSIGAVDE MLKTMMSVSR NELLQKLDPL EQAKVDLVSA YTLNSMFWVY LATQGVNPKE HPVKQELERI RVYMNRVKEI TDKKKAGKLD RGAASRFVKN ALWEPKSKNA SKVANKGKSK S

UniProtKB: Nuclear nucleic acid-binding protein C1D

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Macromolecule #6: Exosome component 10

MacromoleculeName: Exosome component 10 / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAPPSTREPR VLSATSATK S DGEMVLPG FP DADSFVK FAL GSVVAV TKAS GGLPQ FGDEY DFYR SFPGFQ AFC ETQGDRL LQ CMSRVMQY H GCRSNIKDR SKVTELEDKF DLLVDANDV I LERVGILL DE ASGVNKN QQP VLPAGL QVPK TVVSS WNRKA

UniProtKB: Exosome complex component 10

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Macromolecule #7: Exosome complex component CSL4

MacromoleculeName: Exosome complex component CSL4 / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAPPVRYCIP GERLCNLEEG SPGSGTYTRH GYIFSSLAGC LMKSSENGAL PVVSVVRETE SQLLPDVGAI VTCKVSSINS RFAKVHILYV GSMPLKNSFR GTIRKEDVRA TEKDKVEIYK SFRPGDIVLA KVISLGDAQS NYLLTTAENE LGVVVAHSES GIQMVPISWC ...String:
MAPPVRYCIP GERLCNLEEG SPGSGTYTRH GYIFSSLAGC LMKSSENGAL PVVSVVRETE SQLLPDVGAI VTCKVSSINS RFAKVHILYV GSMPLKNSFR GTIRKEDVRA TEKDKVEIYK SFRPGDIVLA KVISLGDAQS NYLLTTAENE LGVVVAHSES GIQMVPISWC EMQCPKTHTK EFRKVARVQP EFLQT

UniProtKB: Exosome complex component CSL4

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Macromolecule #8: Exosome complex component RRP4

MacromoleculeName: Exosome complex component RRP4 / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAMEMRLPVA RKPLSERLGR DTKKHLVVPG DTITTDTGFM RGHGTYMGEE KLIASVAGSV ERVNKLICVK ALKTRYIGEV GDIVVGRITE VQQKRWKVET NSRLDSVLLL SSMNLPGGEL RRRSAEDELA MRGFLQEGDL ISAEVQAVFS DGAVSLHTRS LKYGKLGQGV ...String:
MAMEMRLPVA RKPLSERLGR DTKKHLVVPG DTITTDTGFM RGHGTYMGEE KLIASVAGSV ERVNKLICVK ALKTRYIGEV GDIVVGRITE VQQKRWKVET NSRLDSVLLL SSMNLPGGEL RRRSAEDELA MRGFLQEGDL ISAEVQAVFS DGAVSLHTRS LKYGKLGQGV LVQVSPSLVK RQKTHFHDLP CGASVILGNN GFIWIYPTPE HKEEEAGGFI ANLEPVSLAD REVISRLRNC IISLVTQRMM LYDTSILYCY EASLPHQIKD ILKPEIMEEI VMETRQRLLE QEG

UniProtKB: Exosome complex component RRP4

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Macromolecule #9: Exosome complex component RRP40

MacromoleculeName: Exosome complex component RRP40 / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAEPASVAAE SLAGSRARAA RTVLGQVVLP GEELLLPEQE DAEGPGGAVE RPLSLNARAC SRVRVVCGPG LRRCGDRLLV TKCGRLRHKE PGSGSGGGVY WVDSQQKRYV PVKGDHVIGI VTAKSGDIFK VDVGGSEPAS LSYLSFEGAT KRNRPNVQVG DLIYGQFVVA ...String:
MAEPASVAAE SLAGSRARAA RTVLGQVVLP GEELLLPEQE DAEGPGGAVE RPLSLNARAC SRVRVVCGPG LRRCGDRLLV TKCGRLRHKE PGSGSGGGVY WVDSQQKRYV PVKGDHVIGI VTAKSGDIFK VDVGGSEPAS LSYLSFEGAT KRNRPNVQVG DLIYGQFVVA NKDMEPEMVC IDSCGRANGM GVIGQDGLLF KVTLGLIRKL LAPDCEIIQE VGKLYPLEIV FGMNGRIWVK AKTIQQTLIL ANILEACEHM TSDQRKQIFS RLAES

UniProtKB: Exosome complex component RRP40

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Macromolecule #10: Exosome complex component RRP41

MacromoleculeName: Exosome complex component RRP41 / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG LQLRQTFEAA ILTQLHPRSQ IDIYVQVLQA DGGTYAACVN AATLAVLDAG IPMRDFVCAC SAGFVDGTAL ...String:
MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG LQLRQTFEAA ILTQLHPRSQ IDIYVQVLQA DGGTYAACVN AATLAVLDAG IPMRDFVCAC SAGFVDGTAL ADLSHVEEAA GGPQLALALL PASGQIALLE MDARLHEDHL ERVLEAAAQA ARDVHTLLDR VVRQHVREAS ILLGD

UniProtKB: Exosome complex component RRP41

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Macromolecule #11: Exosome complex component RRP46

MacromoleculeName: Exosome complex component RRP46 / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEEETHTDAK IRAENGTGSS PRGPGCSLRH FACEQNLLSR PDGSASFLQG DTSVLAGVYG PAEVKVSKEI FNKATLEVIL RPKIGLPGVA EKSRERLIRN TCEAVVLGTL HPRTSITVVL QVVSDAGSLL ACCLNAACMA LVDAGVPMRA LFCGVACALD SDGTLVLDPT ...String:
MEEETHTDAK IRAENGTGSS PRGPGCSLRH FACEQNLLSR PDGSASFLQG DTSVLAGVYG PAEVKVSKEI FNKATLEVIL RPKIGLPGVA EKSRERLIRN TCEAVVLGTL HPRTSITVVL QVVSDAGSLL ACCLNAACMA LVDAGVPMRA LFCGVACALD SDGTLVLDPT SKQEKEARAV LTFALDSVER KLLMSSTKGL YSDTELQQCL AAAQAASQHV FRFYRESLQR RYSKS

UniProtKB: Exosome complex component RRP46

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Macromolecule #12: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAPA ALRGRLLCDF RRAPFAGRRR RAPPGGCEER ELALALQEAL EPAVRLGRYP RAQLEVSALL LEDGGSALAA ALTAAALALA ...String:
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAPA ALRGRLLCDF RRAPFAGRRR RAPPGGCEER ELALALQEAL EPAVRLGRYP RAQLEVSALL LEDGGSALAA ALTAAALALA DAGVEMYDLV VGCGLSLAPG PAPTWLLDPT RLEEERAAAG LTVALMPVLN QVAGLLGSGE GGLTESWAEA VRLGLEGCQR LYPVLQQSLV RAARRRGAAA QP

UniProtKB: Exosome complex component MTR3

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Macromolecule #13: Exosome complex component RRP42

MacromoleculeName: Exosome complex component RRP42 / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASVTLSEAE KVYIVHGVQE DLRVDGRGCE DYRCVEVETD VVSNTSGSAR VKLGHTDILV GVKAEMGTPK LEKPNEGYLE FFVDCSASAT PEFEGRGGDD LGTEIANTLY RIFNNKSSVD LKTLCISPRE HCWVLYVDVL LLECGGNLFD AISIAVKAAL FNTRIPRVRV ...String:
MASVTLSEAE KVYIVHGVQE DLRVDGRGCE DYRCVEVETD VVSNTSGSAR VKLGHTDILV GVKAEMGTPK LEKPNEGYLE FFVDCSASAT PEFEGRGGDD LGTEIANTLY RIFNNKSSVD LKTLCISPRE HCWVLYVDVL LLECGGNLFD AISIAVKAAL FNTRIPRVRV LEDEEGSKDI ELSDDPYDCI RLSVENVPCI VTLCKIGYRH VVDATLQEEA CSLASLLVSV TSKGVVTCMR KVGKGSLDPE SIFEMMETGK RVGKVLHASL QSVVHKEESL GPKRQKVGFL G

UniProtKB: Exosome complex component RRP42

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Macromolecule #14: Exosome complex component RRP45

MacromoleculeName: Exosome complex component RRP45 / type: protein_or_peptide / ID: 14 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKETPLSNCE RRFLLRAIEE KKRLDGRQTY DYRNIRISFG TDYGCCIVEL GKTRVLGQVS CELVSPKLNR ATEGILFFNL ELSQMAAPAF EPGRQSDLLV KLNRLMERCL RNSKCIDTES LCVVAGEKVW QIRVDLHLLN HDGNIIDAAS IAAIVALCHF RRPDVSVQGD ...String:
MKETPLSNCE RRFLLRAIEE KKRLDGRQTY DYRNIRISFG TDYGCCIVEL GKTRVLGQVS CELVSPKLNR ATEGILFFNL ELSQMAAPAF EPGRQSDLLV KLNRLMERCL RNSKCIDTES LCVVAGEKVW QIRVDLHLLN HDGNIIDAAS IAAIVALCHF RRPDVSVQGD EVTLYTPEER DPVPLSIHHM PICVSFAFFQ QGTYLLVDPN EREERVMDGL LVIAMNKHRE ICTIQSSGGI MLLKDQVLRC SKIAGVKVAE ITELILKALE NDQKVRKEGG KFGFAESIAN QRITAFKMEK APIDTSDVEE KAEEIIAEAE PPSEVVSTPV LWTPGTAQIG EGVENSWGDL EDSEKEDDEG GGDQAIILDG IKMDTGVEVS DIGSQDAPII LSDSEEEEMI ILEPDKNPKK IRTQTTSAKQ EKAPSKKPVK RRKKKRAAN

UniProtKB: Exosome complex component RRP45

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Macromolecule #15: Exosome complex exonuclease RRP44

MacromoleculeName: Exosome complex exonuclease RRP44 / type: protein_or_peptide / ID: 15 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MLKSKTFLKK TRAGGVMKIV REHYLRDDIG CGAPGCAACG GAHEGPALEP QPQDPASSVC PQPHYLLPDT NVLLHQIDVL EDPAIRNVIV LQTVLQEVRN RSAPVYKRIR DVTNNQEKHF YTFTNEHHRE TYVEQEQGEN ANDRNDRAIR VAAKWYNEHL KKMSADNQLQ ...String:
MLKSKTFLKK TRAGGVMKIV REHYLRDDIG CGAPGCAACG GAHEGPALEP QPQDPASSVC PQPHYLLPDT NVLLHQIDVL EDPAIRNVIV LQTVLQEVRN RSAPVYKRIR DVTNNQEKHF YTFTNEHHRE TYVEQEQGEN ANDRNDRAIR VAAKWYNEHL KKMSADNQLQ VIFITNDRRN KEKAIEEGIP AFTCEEYVKS LTANPELIDR LACLSEEGNE IESGKIIFSE HLPLSKLQQG IKSGTYLQGT FRASRENYLE ATVWIHGDNE ENKEIILQGL KHLNRAVHED IVAVELLPKS QWVAPSSVVL HDEGQNEEDV EKEEETERML KTAVSEKMLK PTGRVVGIIK RNWRPYCGML SKSDIKESRR HLFTPADKRI PRIRIETRQA STLEGRRIIV AIDGWPRNSR YPNGHFVRNL GDVGEKETET EVLLLEHDVP HQPFSQAVLS FLPKMPWSIT EKDMKNREDL RHLCICSVDP PGCTDIDDAL HCRELENGNL EVGVHIADVS HFIRPGNALD QESARRGTTV YLCEKRIDMV PELLSSNLCS LKCDVDRLAF SCIWEMNHNA EILKTKFTKS VINSKASLTY AEAQLRIDSA NMNDDITTSL RGLNKLAKIL KKRRIEKGAL TLSSPEVRFH MDSETHDPID LQTKELRETN SMVEEFMLLA NISVAKKIHE EFSEHALLRK HPAPPPSNYE ILVKAARSRN LEIKTDTAKS LAESLDQAES PTFPYLNTLL RILATRCMMQ AVYFCSGMDN DFHHYGLASP IYTHFTSPIR RYADVIVHRL LAVAIGADCT YPELTDKHKL ADICKNLNFR HKMAQYAQRA SVAFHTQLFF KSKGIVSEEA YILFVRKNAI VVLIPKYGLE GTVFFEEKDK PNPQLIYDDE IPSLKIEDTV FHVFDKVKVK IMLDSSNLQH QKIRMSLVEP QIPGISIPTD TSNMDLNGPK KKKMKLGK

UniProtKB: Exosome complex exonuclease RRP44

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Macromolecule #16: RNA 5 prime hairpin U60

MacromoleculeName: RNA 5 prime hairpin U60 / type: rna / ID: 16
Source (natural)Organism: synthetic construct (others)
SequenceString:
CUACCCCGAG AGGGGUAGUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUU

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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
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: 2.3000000000000003 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.1715 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 angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2356
FSC plot (resolution estimation)

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