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- EMDB-7808: Human nuclear exosome-MTR4 RNA complex - overall reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-7808
TitleHuman nuclear exosome-MTR4 RNA complex - overall reconstruction
Map dataOverall reconstruction for human nuclear exosome-MTR4 helicase complex
Sample
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
    • Protein or peptide: x 13 types
    • RNA: x 1 types
    • Other: x 1 types
  • Ligand: x 3 types
KeywordsRNA exosome / RNA degradation / ribonuclease / helicase / SF2 / RNA-protein complex / translocase / nuclear / HYDROLASE
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 / nuclear polyadenylation-dependent CUT catabolic process ...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 / 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 / negative regulation of telomere maintenance via telomerase / RNA catabolic process / nuclear-transcribed mRNA catabolic process / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / maturation of 5.8S rRNA / nuclear chromosome / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / small-subunit processome / guanyl-nucleotide exchange factor activity / euchromatin / ribosomal small subunit biogenesis / mRNA splicing, via spliceosome / fibrillar center / rRNA processing / chromosome / 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 / RNA helicase / nuclear speck / immune response / nucleotide binding / DNA repair / intracellular membrane-bounded organelle / DNA damage response / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Exosome complex component Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / 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 Rrp43 / : / Mammalian exosome complex component RRP40, N-terminal / 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 / 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 / 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 / Helicase conserved C-terminal domain / 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 / 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 / Exosome complex component RRP42 / Exosome complex component MTR3 / Exosome complex component RRP43 / M-phase phosphoprotein 6 / Exosome complex component RRP41 / Exosome complex component RRP46 ...Exosome RNA helicase MTR4 / Exosome complex component 10 / Exosome complex component RRP45 / Exosome complex component RRP4 / Exosome complex component RRP42 / Exosome complex component MTR3 / Exosome complex component RRP43 / M-phase phosphoprotein 6 / Exosome complex component RRP41 / Exosome complex component RRP46 / Exosome complex component RRP40 / Exosome complex exonuclease RRP44 / Exosome complex component CSL4
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsWeick E-M / Lima CD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118080 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2018
Title: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Authors: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima /
Abstract: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4.
History
DepositionApr 22, 2018-
Header (metadata) releaseMay 16, 2018-
Map releaseJun 20, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6d6q
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7808.png

Downloads & links

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Map

FileDownload / File: emd_7808.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall reconstruction for human nuclear exosome-MTR4 helicase complex
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.08375969 - 0.15396504
Average (Standard dev.)0.00014034889 (±0.0025395288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 410.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z410.880410.880410.880
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0840.1540.000

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Supplemental data

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Sample components

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Entire : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

EntireName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
Components
  • Complex: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
    • Protein or peptide: Exosome complex component RRP45
    • Protein or peptide: Exosome complex component RRP41
    • Protein or peptide: Exosome complex component RRP43
    • Protein or peptide: Exosome complex component RRP46
    • Protein or peptide: Exosome complex component RRP42
    • Protein or peptide: Exosome complex component MTR3
    • Protein or peptide: Exosome complex component RRP40
    • Protein or peptide: Exosome complex component RRP4
    • Protein or peptide: Exosome complex component CSL4
    • Protein or peptide: Exosome component 10
    • Protein or peptide: Exosome complex exonuclease RRP44
    • Protein or peptide: M-phase phosphoprotein 6
    • Protein or peptide: Exosome RNA helicase MTR4
    • RNA: RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')
    • Other: DNA/RNA (62-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...

SupramoleculeName: Human nuclear exosome-MTR4 helicase captured after unwinding a DNA/RNA substrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Details: Human C1D/Rrp47 also in the sample, but was not observed in density
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 690 KDa

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Macromolecule #1: Exosome complex component RRP45

MacromoleculeName: Exosome complex component RRP45 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.82802 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPNSHMKE TPLSNCERRF LLRAIEEKKR LDGRQTYDYR NIRISFGTDY GCCIVELGKT RVLGQVSCEL VSPKLNRAT EGILFFNLEL SQMAAPAFEP GRQSDLLVKL NRLMERCLRN SKCIDTESLC VVAGEKVWQI RVDLHLLNHD G NIIDAASI ...String:
MGSSHHHHHH SQDPNSHMKE TPLSNCERRF LLRAIEEKKR LDGRQTYDYR NIRISFGTDY GCCIVELGKT RVLGQVSCEL VSPKLNRAT EGILFFNLEL SQMAAPAFEP GRQSDLLVKL NRLMERCLRN SKCIDTESLC VVAGEKVWQI RVDLHLLNHD G NIIDAASI AAIVALCHFR RPDVSVQGDE VTLYTPEERD PVPLSIHHMP ICVSFAFFQQ GTYLLVDPNE REERVMDGLL VI AMNKHRE ICTIQSSGGI MLLKDQVLRC SKIAGVKVAE ITELILKALE NDQKVRKEGG KFGFAESIAN QRITAFKMEK API DTSDVE EKAEEIIAEA EPPSEVVSTP VLWTPGTAQI GEGVENSWGD LEDSEKEDDE GGGDQAIILD GIKMDTGVEV SDIG SQELG FHHVGQTGLE FLTSDAPIIL SDSEEEEMII LEPDKNPKKI RTQTTSAKQE KAPSKKPVKR RKKKRAAN

UniProtKB: Exosome complex component RRP45

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Macromolecule #2: Exosome complex component RRP41

MacromoleculeName: Exosome complex component RRP41 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.831473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADPMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARAL PDRALVNCQY SSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL HPRSQIDIYV QVLQADGGTY AACVNAATLA VLDAGIPMRD F VCACSAGF ...String:
MADPMAGLEL LSDQGYRVDG RRAGELRKIQ ARMGVFAQAD GSAYIEQGNT KALAVVYGPH EIRGSRARAL PDRALVNCQY SSATFSTGE RKRRPHGDRK SCEMGLQLRQ TFEAAILTQL HPRSQIDIYV QVLQADGGTY AACVNAATLA VLDAGIPMRD F VCACSAGF VDGTALADLS HVEEAAGGPQ LALALLPASG QIALLEMDAR LHEDHLERVL EAAAQAARDV HTLLDRVVRQ HV REASILL GD

UniProtKB: Exosome complex component RRP41

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Macromolecule #3: Exosome complex component RRP43

MacromoleculeName: Exosome complex component RRP43 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.285762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFAA PSTDAPDKGY VVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ IIQKEDLCIS PGKLVWVLYC DLICLDYDGN ILDACTFALL A ALKNVQLP ...String:
DPMAAGFKTV EPLEYYRRFL KENCRPDGRE LGEFRTTTVN IGSISTADGS ALVKLGNTTV ICGVKAEFAA PSTDAPDKGY VVPNVDLPP LCSSRFRSGP PGEEAQVASQ FIADVIENSQ IIQKEDLCIS PGKLVWVLYC DLICLDYDGN ILDACTFALL A ALKNVQLP EVTINEETAL AEVNLKKKSY LNIRTHPVAT SFAVFDDTLL IVDPTGEEEH LATGTLTIVM DEEGKLCCLH KP GGSGLTG AKLQDCMSRA VTRHKEVKKL MDEVIKSMKP K

UniProtKB: Exosome complex component RRP43

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Macromolecule #4: Exosome complex component RRP46

MacromoleculeName: Exosome complex component RRP46 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.480213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVSK EIFNKATLEV ILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT VVLQVVSDAG SLLACCLNAA CMALVDAGVP MRALFCGVAC A LDSDGTLV ...String:
SLMEEETHTD AKIRAENGTG SSPRGPGCSL RHFACEQNLL SRPDGSASFL QGDTSVLAGV YGPAEVKVSK EIFNKATLEV ILRPKIGLP GVAEKSRERL IRNTCEAVVL GTLHPRTSIT VVLQVVSDAG SLLACCLNAA CMALVDAGVP MRALFCGVAC A LDSDGTLV LDPTSKQEKE ARAVLTFALD SVERKLLMSS TKGLYSDTEL QQCLAAAQAA SQHVFRFYRE SLQRRYSKS

UniProtKB: Exosome complex component RRP46

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Macromolecule #5: Exosome complex component RRP42

MacromoleculeName: Exosome complex component RRP42 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.072633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMASVTLSE AEKVYIVHGV QEDLRVDGRG CEDYRCVEVE TDVVSNTSGS ARVKLGHTDI LVGVKAEMGT PKLEKPNEGY LEFFVDCSA SATPEFEGRG GDDLGTEIAN TLYRIFNNKS SVDLKTLCIS PREHCWVLYV DVLLLECGGN LFDAISIAVK A ALFNTRIP ...String:
DPMASVTLSE AEKVYIVHGV QEDLRVDGRG CEDYRCVEVE TDVVSNTSGS ARVKLGHTDI LVGVKAEMGT PKLEKPNEGY LEFFVDCSA SATPEFEGRG GDDLGTEIAN TLYRIFNNKS SVDLKTLCIS PREHCWVLYV DVLLLECGGN LFDAISIAVK A ALFNTRIP RVRVLEDEEG SKDIELSDDP YDCIRLSVEN VPCIVTLCKI GYRHVVDATL QEEACSLASL LVSVTSKGVV TC MRKVGKG SLDPESIFEM METGKRVGKV LHASLQSVVH KEESLGPKRQ KVGFLG

UniProtKB: Exosome complex component RRP42

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Macromolecule #6: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.267127 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE RELALALQEA LEPAVRLGRY PRAQLEVSAL LLEDGGSALA A ALTAAALA ...String:
MPGDHRRIRG PEESQPPQLY AADEEEAPGT RDPTRLRPVY ARAGLLSQAK GSAYLEAGGT KVLCAVSGPR QAEGGERGGG PAGAGGEAP AALRGRLLCD FRRAPFAGRR RRAPPGGCEE RELALALQEA LEPAVRLGRY PRAQLEVSAL LLEDGGSALA A ALTAAALA LADAGVEMYD LVVGCGLSLA PGPAPTWLLD PTRLEEERAA AGLTVALMPV LNQVAGLLGS GEGGLTESWA EA VRLGLEG CQRLYPVLQQ SLVRAARRRG AAAQP

UniProtKB: Exosome complex component MTR3

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Macromolecule #7: Exosome complex component RRP40

MacromoleculeName: Exosome complex component RRP40 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.796371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAEPASVA AESLAGSRAR AARTVLGQVV LPGEELLLPE QEDAEGPGGA VERPLSLNAR ACSRVRVVCG PGLRRCGDRL LVTKCGRLR HKEPGSGSGG GVYWVDSQQK RYVPVKGDHV IGIVTAKSGD IFKVDVGGSE PASLSYLSFE GATKRNRPNV Q VGDLIYGQ ...String:
DPMAEPASVA AESLAGSRAR AARTVLGQVV LPGEELLLPE QEDAEGPGGA VERPLSLNAR ACSRVRVVCG PGLRRCGDRL LVTKCGRLR HKEPGSGSGG GVYWVDSQQK RYVPVKGDHV IGIVTAKSGD IFKVDVGGSE PASLSYLSFE GATKRNRPNV Q VGDLIYGQ FVVANKDMEP EMVCIDSCGR ANGMGVIGQD GLLFKVTLGL IRKLLAPDCE IIQEVGKLHP LEIVFGMNGR IW VKAKTIQ QTLILANILE ACEHMTSDQR KQIFSRLAES

UniProtKB: Exosome complex component RRP40

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Macromolecule #8: Exosome complex component RRP4

MacromoleculeName: Exosome complex component RRP4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.184371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPHMAMEMRL PVARKPLSER LGRDTKKHLV VPGDTITTDT GFMRGHGTYM GEEKLIASVA GSVERVNKLI CVKALKTRYI GEVGDIVVG RITEVQQKRW KVETNSRLDS VLLLSSMNLP GGELRRRSAE DELAMRGFLQ EGDLISAEVQ AVFSDGAVSL H TRSLKYGK ...String:
DPHMAMEMRL PVARKPLSER LGRDTKKHLV VPGDTITTDT GFMRGHGTYM GEEKLIASVA GSVERVNKLI CVKALKTRYI GEVGDIVVG RITEVQQKRW KVETNSRLDS VLLLSSMNLP GGELRRRSAE DELAMRGFLQ EGDLISAEVQ AVFSDGAVSL H TRSLKYGK LGQGVLVQVS PSLVKRQKTH FHDLPCGASV ILGNNGFIWI YPTPEHKEEE AGGFIANLEP VSLADREVIS RL RNCIISL VTQRMMLYDT SILYCYEASL PHQIKDILKP EIMEEIVMET RQRLLEQEG

UniProtKB: Exosome complex component RRP4

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Macromolecule #9: Exosome complex component CSL4

MacromoleculeName: Exosome complex component CSL4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.690971 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DPMAPPVRYC IPGERLCNLE EGSPGSGTYT RHGYIFSSLA GCLMKSSENG ALPVVSVVRE TESQLLPDVG AIVTCKVSSI NSRFAKVHI LYVGSMPLKN SFRGTIRKED VRATEKDKVE IYKSFRPGDI VLAKVISLGD AQSNYLLTTA ENELGVVVAH S ESGIQMVP ...String:
DPMAPPVRYC IPGERLCNLE EGSPGSGTYT RHGYIFSSLA GCLMKSSENG ALPVVSVVRE TESQLLPDVG AIVTCKVSSI NSRFAKVHI LYVGSMPLKN SFRGTIRKED VRATEKDKVE IYKSFRPGDI VLAKVISLGD AQSNYLLTTA ENELGVVVAH S ESGIQMVP ISWCEMQCPK THTKEFRKVA RVQPEFLQT

UniProtKB: Exosome complex component CSL4

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Macromolecule #10: Exosome component 10

MacromoleculeName: Exosome component 10 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.754859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAPPSTREP RVLSATSATK SDGEMVLPGF PDADSFVKFA LGSVVAVTKA SGGLPQFGDE YDFYRSFPGF QAFCETQGDR LLQCMSRVM QYHGCRSNIK DRSKVTELED KFDLLVDAND VILERVGILL DEASGVNKNQ QPVLPAGLQV PKTVVSSWNR K AAEYGKKA ...String:
SMAPPSTREP RVLSATSATK SDGEMVLPGF PDADSFVKFA LGSVVAVTKA SGGLPQFGDE YDFYRSFPGF QAFCETQGDR LLQCMSRVM QYHGCRSNIK DRSKVTELED KFDLLVDAND VILERVGILL DEASGVNKNQ QPVLPAGLQV PKTVVSSWNR K AAEYGKKA KSETFRLLHA KNIIRPQLKF REKIDNSNTP FLPKIFIKPN AQKPLPQALS KERRERPQDR PEDLDVPPAL AD FIHQQRT QQVEQDMFAH PYQYELNHFT PADAVLQKPQ PQLYRPIEET PCHFISSLDE LVELNEKLLN CQEFAVNLEH HSY RSFLGL TCLMQISTRT EDFIIDTLEL RSDMYILNES LTDPAIVKVF HGADSDIEWL QKDFGLYVVN MFDTHQAARL LNLG RHSLD HLLKLYCNVD SNKQYQLADW RIRPLPEEML SYARDDTHYL LYIYDKMRLE MWERGNGQPV QLQVVWQRSR DICLK KFIK PIFTDESYLE LYRKQKKHLN TQQLTAFQLL FAWRDKTARR EDESYGYVLP NHMMLKIAEE LPKEPQGIIA CCNPVP PLV RQQINEMHLL IQQAREMPLL KSEVAAGVKK SGPLPSAERL ENVLFGPHDC SHAPPDGYPI IPTSGSVPVQ KQASLFP DE KEDNLLGSRG SGSGSGSGSV SQAAKFDPST KIYEISNRWK LAQVQVQKDS KEAVKKKAAE QTAAREQAKE ACKAAAEQ A ISVRQQVVLE NAAKKRERAT SDPRTTEQKQ EKKRLKISKK

UniProtKB: Exosome complex component 10, Exosome complex component 10

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Macromolecule #11: Exosome complex exonuclease RRP44

MacromoleculeName: Exosome complex exonuclease RRP44 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.26793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMLKSKTFL KKTRAGGVMK IVREHYLRDD IGCGAPGCAA CGGAHEGPAL EPQPQDPASS VCPQPHYLLP DTNVLLHQID VLEDPAIRN VIVLQTVLQE VRNRSAPVYK RIRDVTNNQE KHFYTFTNEH HRETYVEQEQ GENANDRNNR AIRVAAKWYN E HLKKMSAD ...String:
GSMLKSKTFL KKTRAGGVMK IVREHYLRDD IGCGAPGCAA CGGAHEGPAL EPQPQDPASS VCPQPHYLLP DTNVLLHQID VLEDPAIRN VIVLQTVLQE VRNRSAPVYK RIRDVTNNQE KHFYTFTNEH HRETYVEQEQ GENANDRNNR AIRVAAKWYN E HLKKMSAD NQLQVIFITN DRRNKEKAIE EGIPAFTCEE YVKSLTANPE LIDRLACLSE EGNEIESGKI IFSEHLPLSK LQ QGIKSGT YLQGTFRASR ENYLEATVWI HGDSEENKEI ILQGLKHLNR AVHEDIVAVE LLPKSQWVAP SSVVLHDEGQ NEE DVEKEE ETERMLKTAV SEKMLKPTGR VVGIIKRNWR PYCGMLSKSD IKESRRHLFT PADKRIPRIR IETRQASTLE GRRI IVAID GWPRNSRYPN GHFVRNLGDV GEKETETEVL LLEHDVPHQP FSQAVLSFLP KMPWSITEKD MKNREDLRHL CICSV DPPG CTDINDALHC RELENGNLEV GVHIADVSHF IRPGNALDQE SARRGTTVYL CEKRIDMVPE LLSSNLCSLK CDVDRL AFS CIWEMNHNAE ILKTKFTKSV INSKASLTYA EAQLRIDSAN MNDDITTSLR GLNKLAKILK KRRIEKGALT LSSPEVR FH MDSETHDPID LQTKELRETN SMVEEFMLLA NISVAKKIHE EFSEHALLRK HPAPPPSNYE ILVKAARSRN LEIKTDTA K SLAESLDQAE SPTFPYLNTL LRILATRCMM QAVYFCSGMD NDFHHYGLAS PIYTHFTSPI RRYADVIVHR LLAVAIGAD CTYPELTDKH KLADICKNLN FRHKMAQYAQ RASVAFHTQL FFKSNGIVSE EAYILFVRKN AIVVLIPKYG LEGTVFFEEK DKPNPQLIY DDEIPSLKIE DTVFHVFDKV KVKIMLDSSN LQHQKIRMSL VEPQIPGISI PTDTSNMDLN GPKKKKMKLG K

UniProtKB: Exosome complex exonuclease RRP44

+
Macromolecule #12: M-phase phosphoprotein 6

MacromoleculeName: M-phase phosphoprotein 6 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.267961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DPMAAERKTR LSKNLLRMKF MQRGLDSETK KQLEEEEKKI ISEEHWYLDL PELKEKESFI IEEQSFLLCE DLLYGRMSFR GFNPEVEKL MLQMNAKHKA EEVEDETVEL DVSDEEMARR YETLVGTIGK KFARKRDHAN YEEDENGDIT PIKAKKMFLK P QD

UniProtKB: M-phase phosphoprotein 6

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Macromolecule #13: Exosome RNA helicase MTR4

MacromoleculeName: Exosome RNA helicase MTR4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.224961 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA ...String:
SGDMADAFGD ELFSVFEGDS TTAAGTKKDK EKDKGKWKGP PGSADKAGKR FDGKLQSEST NNGKNKRDVD FEGTDEPIFG KKPRIEESI TEDLSLADLM PRVKVQSVET VEGCTHEVAL PAEEDYLPLK PRVGKAAKEY PFILDAFQRE AIQCVDNNQS V LVSAHTSA GKTVCAEYAI ALALREKQRV IFTSPIKALS NQKYREMYEE FQDVGLMTGD VTINPTASCL VMTTEILRSM LY RGSEVMR EVAWVIFDEI HYMRDSERGV VWEETIILLP DNVHYVFLSA TIPNARQFAE WICHLHKQPC HVIYTDYRPT PLQ HYIFPA GGDGLHLVVD ENGDFREDNF NTAMQVLRDA GDLAKGDQKG RKGGTKGPSN VFKIVKMIME RNFQPVIIFS FSKK DCEAY ALQMTKLDFN TDEEKKMVEE VFSNAIDCLS DEDKKLPQVE HVLPLLKRGI GIHHGGLLPI LKETIEILFS EGLIK ALFA TETFAMGINM PARTVLFTNA RKFDGKDFRW ISSGEYIQMS GRAGRRGMDD RGIVILMVDE KMSPTIGKQL LKGSAD PLN SAFHLTYNMV LNLLRVEEIN PEYMLEKSFY QFQHYRAIPG VVEKVKNSEE QYNKIVIPNE ESVVIYYKIR QQLAKLG KE IEEYIHKPKY CLPFLQPGRL VKVKNEGDDF GWGVVVNFSK KSNVKPNSGE LDPLYVVEVL LRCSKESLKN SATEAAKP A KPDEKGEMQV VPVLVHLLSA ISSVRLYIPK DLRPVDNRQS VLKSIQEVQK RFPDGIPLLD PIDDMGIQDQ GLKKVIQKV EAFEHRMYSH PLHNDPNLET VYTLCEKKAQ IAIDIKSAKR ELKKARTVLQ MDELKCRKRV LRRLGFATSS DVIEMKGRVA CEISSADEL LLTEMMFNGL FNDLSAEQAT ALLSCFVFQE NSSEMPKLTE QLAGPLRQMQ ECAKRIAKVS AEAKLEIDEE T YLSSFKPH LMDVVYTWAT GATFAHICKM TDVFEGSIIR CMRRLEELLR QMCQAAKAIG NTELENKFAE GITKIKRDIV FA ASLYL

UniProtKB: Exosome RNA helicase MTR4

+
Macromolecule #14: RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')

MacromoleculeName: RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')
type: rna / ID: 14 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.143175 KDa
SequenceString:
AGCACCGUAA AGACGC

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Macromolecule #15: DNA/RNA (62-MER)

MacromoleculeName: DNA/RNA (62-MER) / type: other / ID: 15 / Number of copies: 1
Classification: polydeoxyribonucleotide/polyribonucleotide hybrid
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.487074 KDa
SequenceString:
(DG)(DC)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DC) (DG)(DG)(DT)(DG)(DC)(DT)CACC ACACCACACC AC ACCACAC CACACCACAC CACACAAAAA AAA

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Macromolecule #16: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 16 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #17: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 17 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #18: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 18 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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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

Concentration1.0 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
100.0 mMsodium chlorideNaClSodium chloride
0.5 mMmagnesium chlorideMgCl2
2.0 mMAMPPNP
1.0 mMBME
0.05 %ChapsoCHAPS detergent
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa
VitrificationCryogen name: ETHANE / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 30 sec wait time, 2.5 sec blot time.
DetailsSample was monodisperse upon elution from gel filtration prior to vitrification.

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1439 / Average electron dose: 85.23 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 278185
Startup modelType of model: NONE / Details: Ab initio model determination
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.1) / Software - details: from 0.6.1 to 0.6.5
Final 3D classificationNumber classes: 4 / Avg.num./class: 271036 / Software - Name: RELION (ver. 2.1b1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1)
Details: Focused refinements with five strategies required to achieve final model
Number images used: 122703
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModels were rebuilt manually using Coot, with real space refinement with local scaling followed by Phenix real space refinement with suboptimal global scaling.
RefinementSpace: REAL / Protocol: BACKBONE TRACE / Overall B value: 73.6 / Target criteria: Correlation coefficient
Output model

PDB-6d6q:
Human nuclear exosome-MTR4 RNA complex - overall reconstruction

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