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- EMDB-4301: Structure of the nuclear RNA exosome -

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Basic information

Entry
Database: EMDB / ID: EMD-4301
TitleStructure of the nuclear RNA exosome
Map dataStructure of the nuclear RNA exosome
Sample
  • Complex: Nuclear RNA exosome
    • Complex: Nuclear RNA exosome
      • Protein or peptide: x 14 types
    • Complex: nucleic acid
      • RNA: x 1 types
Function / homology
Function and homology information


nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / 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) / : / 3'-5' RNA helicase activity / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / rRNA primary transcript binding / poly(A) binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / poly(U) RNA binding / maturation of 5.8S rRNA / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / enzyme regulator activity / RNA endonuclease activity / mRNA processing / double-stranded RNA binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / manganese ion binding / 3'-5'-RNA exonuclease activity / double-stranded DNA binding / regulation of gene expression / endonuclease activity / tRNA binding / RNA helicase activity / single-stranded RNA binding / oxidoreductase activity / RNA helicase / nucleotide binding / mRNA binding / protein-containing complex binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Exosome-associated factor Rrp47/DNA strand repair C1D / M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain ...Exosome-associated factor Rrp47/DNA strand repair C1D / M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / 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 / Sas10/Utp3/C1D / Sas10/Utp3/C1D family / 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 / Prismane-like 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 / S1 domain profile. / 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 complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / ATP-dependent RNA helicase DOB1 / Exosome complex component MTR3 / Exosome complex component RRP46 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / Exosome complex component RRP45 ...Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex protein LRP1 / Exosome complex component SKI6 / ATP-dependent RNA helicase DOB1 / Exosome complex component MTR3 / Exosome complex component RRP46 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Exosome complex exonuclease RRP6 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSchuller JM / Falk S / Conti E
Funding support Belgium, 1 items
OrganizationGrant numberCountry
ERCEXORICO Belgium
CitationJournal: Science / Year: 2018
Title: Structure of the nuclear exosome captured on a maturing preribosome.
Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti /
Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation.
History
DepositionFeb 20, 2018-
Header (metadata) releaseMar 14, 2018-
Map releaseMar 21, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fsz
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4301.png

Downloads & links

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Map

FileDownload / File: emd_4301.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the nuclear RNA exosome
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.047356263 - 0.11682776
Average (Standard dev.)0.00011799472 (±0.00213669)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 594.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z594.000594.000594.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0470.1170.000

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Supplemental data

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Sample components

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Entire : Nuclear RNA exosome

EntireName: Nuclear RNA exosome
Components
  • Complex: Nuclear RNA exosome
    • Complex: Nuclear RNA exosome
      • Protein or peptide: Exosome complex component RRP45
      • Protein or peptide: Exosome complex component SKI6
      • 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 complex exonuclease DIS3
      • Protein or peptide: Exosome complex exonuclease RRP6
      • Protein or peptide: Exosome complex protein LRP1
      • Protein or peptide: ATP-dependent RNA helicase DOB1
      • Protein or peptide: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
    • Complex: nucleic acid
      • RNA: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')

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Supramolecule #1: Nuclear RNA exosome

SupramoleculeName: Nuclear RNA exosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Nuclear RNA exosome

SupramoleculeName: Nuclear RNA exosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#15
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: nucleic acid

SupramoleculeName: nucleic acid / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP...

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.158137 KDa
SequenceString:
AAAAUUUAAA UUUUUUUUUU UUU

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Macromolecule #2: Exosome complex component RRP45

MacromoleculeName: Exosome complex component RRP45 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 33.79959 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KDIEISASES KFILEALRQN YRLDGRSFDQ FRDVEITFGK EFGDVSVKMG NTKVHCRISC QIAQPYEDRP FEGLFVISTE ISPMAGSQF ENGNITGEDE VLCSRIIEKS VRRSGALDVE GLCIVAGSKC WAVRADVHFL DCDGGFIDAS CIAVMAGLMH F KKPDITVH ...String:
KDIEISASES KFILEALRQN YRLDGRSFDQ FRDVEITFGK EFGDVSVKMG NTKVHCRISC QIAQPYEDRP FEGLFVISTE ISPMAGSQF ENGNITGEDE VLCSRIIEKS VRRSGALDVE GLCIVAGSKC WAVRADVHFL DCDGGFIDAS CIAVMAGLMH F KKPDITVH GEQIIVHPVN EREPVPLGIL HIPICVTFSF FNPQDTEENI KGETNSEISI IDATLKEELL RDGVLTVTLN KN REVVQVS KAGGLPMDAL TLMKCCHEAY SIIEKITDQI LQLLKEDSEK RNKYAAMLTS ENAREI

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Macromolecule #3: Exosome complex component SKI6

MacromoleculeName: Exosome complex component SKI6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.794926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMSRLEIYS PEGLRLDGRR WNELRRFESS INTHPHAADG SSYMEQGNNK IITLVKGPKE PRLKSQMDTS KALLNVSVNI TKFSKFERS KSSHKNERRV LEIQTSLVRM FEKNVMLNIY PRTVIDIEIH VLEQDGGIMG SLINGITLAL IDAGISMFDY I SGISVGLY ...String:
GHMSRLEIYS PEGLRLDGRR WNELRRFESS INTHPHAADG SSYMEQGNNK IITLVKGPKE PRLKSQMDTS KALLNVSVNI TKFSKFERS KSSHKNERRV LEIQTSLVRM FEKNVMLNIY PRTVIDIEIH VLEQDGGIMG SLINGITLAL IDAGISMFDY I SGISVGLY DTTPLLDTNS LEENAMSTVT LGVVGKSEKL SLLLVEDKIP LDRLENVLAI GIAGAHRVRD LMDEELRKHA QK RVSNASA R

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Macromolecule #4: Exosome complex component RRP43

MacromoleculeName: Exosome complex component RRP43 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 43.977805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AESTTLETIE IHPITFPPEV LARISPELSL QRHLSLGIRP CLRKYEEFRD VAIENNTLSR YADAGNIDTK NNILGSNVLK SGKTIVITS ITGGIIEETS ASIKDLDDFG EEELFEVTKE EDIIANYASV YPVVEVERGR VGACTDEEMT ISQKLHDSIL H SRILPKKA ...String:
AESTTLETIE IHPITFPPEV LARISPELSL QRHLSLGIRP CLRKYEEFRD VAIENNTLSR YADAGNIDTK NNILGSNVLK SGKTIVITS ITGGIIEETS ASIKDLDDFG EEELFEVTKE EDIIANYASV YPVVEVERGR VGACTDEEMT ISQKLHDSIL H SRILPKKA LKVKAGVRSA NEDGTFSVLY PDELEDDTLN ETNLKMKRKW SYVLYAKIVV LSRTGPVFDL CWNSLMYALQ SV KLPRAFI DERASDLRMT IRTRGRSATI RETYEIICDQ TKSVPLMINA KNIAFASNYG IVELDPECQL QNSDNSEEEE VDI DMDKLN TVLIADLDTE AEETSIHSTI SILAAPSGNY KQLTLMGGGA KITPEMIKRS LLLSRVRADD LSTRFNI

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Macromolecule #5: Exosome complex component RRP46

MacromoleculeName: Exosome complex component RRP46 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.913988 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHGNNKEPNT KNRLDSAEKK KKMSVQAEIG ILDHVDGSSE FVSQDTKVIC SVTGPIEPKA RQELPTQLAL EIIVRPAKGV ATTREKVLE DKLRAVLTPL ITRHCYPRQL CQITCQILES GEDEAEFSLR ELSCCINAAF LALVDAGIAL NSMCASIPIA I IKDTSDII ...String:
GHGNNKEPNT KNRLDSAEKK KKMSVQAEIG ILDHVDGSSE FVSQDTKVIC SVTGPIEPKA RQELPTQLAL EIIVRPAKGV ATTREKVLE DKLRAVLTPL ITRHCYPRQL CQITCQILES GEDEAEFSLR ELSCCINAAF LALVDAGIAL NSMCASIPIA I IKDTSDII VDPTAEQLKI SLSVHTLALE FVNGGKVVKN VLLLDSNGDF NEDQLFSLLE LGEQKCQELV TNIRRIIQDN IS PRLVV

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Macromolecule #6: Exosome complex component RRP42

MacromoleculeName: Exosome complex component RRP42 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 29.294398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMSLSVAEK SYLYDSLAST PSIRPDGRLP HQFRPIEIFT DFLPSSNGSS RIIASDGSEC IVSIKSKVVD HHVENELLQV DVDIAGQRD DALVVETITS LLNKVLKSGS GVDSSKLQLT KKYSFKIFVD VLVISSHSHP ISLISFAIYS ALNSTYLPKL I SAFDDLEV ...String:
GHMSLSVAEK SYLYDSLAST PSIRPDGRLP HQFRPIEIFT DFLPSSNGSS RIIASDGSEC IVSIKSKVVD HHVENELLQV DVDIAGQRD DALVVETITS LLNKVLKSGS GVDSSKLQLT KKYSFKIFVD VLVISSHSHP ISLISFAIYS ALNSTYLPKL I SAFDDLEV EELPTFHDYD MVKLDINPPL VFILAVVGNN MLLDPAANES EVANNGLIIS WSNGKITSPI RSVALNDSNV KS FKPHLLK QGLAMVEKYA PDVVRSLENL

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Macromolecule #7: Exosome complex component MTR3

MacromoleculeName: Exosome complex component MTR3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.559869 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNVQDRRRLL GPAAAKPMAF SNTTTHVPEK KSTDLTPKGN ESEQELSLHT GFIENCNGSA LVEARSLGHQ TSLISAVYGP RSIRGSFTS QGTISIQLKN GLLEKYNTNE LKEVSSFLMG IFNSVVNLSR YPKSGIDIFV YLTYDKDLTN NPQDDDSQSK M TSSQISSL ...String:
MNVQDRRRLL GPAAAKPMAF SNTTTHVPEK KSTDLTPKGN ESEQELSLHT GFIENCNGSA LVEARSLGHQ TSLISAVYGP RSIRGSFTS QGTISIQLKN GLLEKYNTNE LKEVSSFLMG IFNSVVNLSR YPKSGIDIFV YLTYDKDLTN NPQDDDSQSK M TSSQISSL IPHCITSITL ALADAGIELV DMAGAGEANG TVVSFIKNGE EIVGFWKDDG DDEDLLECLD RCKEQYNRYR DL MISCLMN QET

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Macromolecule #8: Exosome complex component RRP40

MacromoleculeName: Exosome complex component RRP40 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.778551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMSTFIFPG DSFPVDPTTP VKLGPGIYCD PNTQEIRPVN TGVLHVSAKG KSGVQTAYID YSSKRYIPSV NDFVIGVIIG TFSDSYKVS LQNFSSSVSL SYMAFPNASK KNRPTLQVGD LVYARVCTAE KELEAEIECF DSTTGRDAGF GILEDGMIID V NLNFARQL ...String:
GHMSTFIFPG DSFPVDPTTP VKLGPGIYCD PNTQEIRPVN TGVLHVSAKG KSGVQTAYID YSSKRYIPSV NDFVIGVIIG TFSDSYKVS LQNFSSSVSL SYMAFPNASK KNRPTLQVGD LVYARVCTAE KELEAEIECF DSTTGRDAGF GILEDGMIID V NLNFARQL LFNNDFPLLK VLAAHTKFEV AIGLNGKIWV KCEELSNTLA CYRTIMECCQ KNDTAAFKDI AKRQFKEILT VK EE

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Macromolecule #9: Exosome complex component RRP4

MacromoleculeName: Exosome complex component RRP4 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.714445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RSMSEVITIT KRNGAFQNSS NLSYNNTGIS DDENDEEDIY MHDVNSASKS ESDSQIVTPG ELVTDDPIWM RGHGTYFLDN MTYSSVAGT VSRVNRLLSV IPLKGRYAPE TGDHVVGRIA EVGNKRWKVD IGGKQHAVLM LGSVNLPGGI LRRKSESDEL Q MRSFLKEG ...String:
RSMSEVITIT KRNGAFQNSS NLSYNNTGIS DDENDEEDIY MHDVNSASKS ESDSQIVTPG ELVTDDPIWM RGHGTYFLDN MTYSSVAGT VSRVNRLLSV IPLKGRYAPE TGDHVVGRIA EVGNKRWKVD IGGKQHAVLM LGSVNLPGGI LRRKSESDEL Q MRSFLKEG DLLNAEVQSL FQDGSASLHT RSLKYGKLRN GMFCQVPSSL IVRAKNHTHN LPGNITVVLG VNGYIWLRKT SQ MDLARDT PSANNSSSIK STGPTGAVSL NPSITRLEEE SSWQIYSDEN DPSISNNIRQ AICRYANVIK ALAFCEIGIT QQR IVSAYE ASMVYSNVGE LIEKNVMESI GSDILTAEKM RGNGN

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Macromolecule #10: Exosome complex component CSL4

MacromoleculeName: Exosome complex component CSL4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 32.805645 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHHHHHHPM ACNFQFPEIA YPGKLICPQY GTENKDGEDI IFNYVPGPGT KLIQYEHNGR TLEAITATLV GTVRCEEEKK TDQEEEREG TDQSTEEEKS VDASPNDVTR RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR A NVEILAVE ...String:
MKHHHHHHPM ACNFQFPEIA YPGKLICPQY GTENKDGEDI IFNYVPGPGT KLIQYEHNGR TLEAITATLV GTVRCEEEKK TDQEEEREG TDQSTEEEKS VDASPNDVTR RTVKNILVSV LPGTEKGRKT NKYANNDFAN NLPKEGDIVL TRVTRLSLQR A NVEILAVE DKPSPIDSGI GSNGSGIVAA GGGSGAATFS VSQASSDLGE TFRGIIRSQD VRSTDRDRVK VIECFKPGDI VR AQVLSLG DGTNYYLTTA RNDLGVVFAR AANGAGGLMY ATDWQMMTSP VTGATEKRKC AKPF

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Macromolecule #11: Exosome complex exonuclease DIS3

MacromoleculeName: Exosome complex exonuclease DIS3 / 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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 113.983898 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMSVPAIAP RRKRLADGLS VTQKVFVRSR NGGATKIVRE HYLRSDIPCL SRSCTKCPQI VVPDAQNELP KFILSDSPLE LSAPIGKHY VVLDTNVVLQ AIDLLENPNC FFDVIVPQIV LDEVRNKSYP VYTRLRTLCR DSDDHKRFIV FHNEFSEHTF V ERLPNETI ...String:
GAMSVPAIAP RRKRLADGLS VTQKVFVRSR NGGATKIVRE HYLRSDIPCL SRSCTKCPQI VVPDAQNELP KFILSDSPLE LSAPIGKHY VVLDTNVVLQ AIDLLENPNC FFDVIVPQIV LDEVRNKSYP VYTRLRTLCR DSDDHKRFIV FHNEFSEHTF V ERLPNETI NDRNNRAIRK TCQWYSEHLK PYDINVVLVT NDRLNREAAT KEVESNIITK SLVQYIELLP NADDIRDSIP QM DSFDKDL ERDTFSDFTF PEYYSTARVM GGLKNGVLYQ GNIQISEYNF LEGSVSLPRF SKPVLIVGQK NLNRAFNGDQ VIV ELLPQS EWKAPSSIVL DSEHFDVNDN PDIEAGDDDD NNESSSNTTV ISDKQRRLLA KDAMIAQRSK KIQPTAKVVY IQRR SWRQY VGQLAPSSVD PQSSSTQNVF VILMDKCLPK VRIRTRRAAE LLDKRIVISI DSWPTTHKYP LGHFVRDLGT IESAQ AETE ALLLEHDVEY RPFSKKVLEC LPAEGHDWKA PTKLDDPEAV SKDPLLTKRK DLRDKLICSI DPPGCVDIND ALHAKK LPN GNWEVGVHIA DVTHFVKPGT ALDAEGAARG TSVYLVDKRI DMLPMLLGTD LCSLKPYVDR FAFSVIWELD DSANIVN VN FMKSVIRSRE AFSYEQAQLR IDDKTQNDEL TMGMRALLKL SVKLKQKRLE AGALNLASPE VKVHMDSETS DPNEVEIK K LLATNSLVEE FMLLANISVA RKIYDAFPQT AMLRRHAAPP STNFEILNEM LNTRKNMSIS LESSKALADS LDRCVDPED PYFNTLVRIM STRCMMAAQY FYSGAYSYPD FRHYGLAVDI YTHFTSPIRR YCDVVAHRQL AGAIGYEPLS LTHRDKNKMD MICRNINRK HRNAQFAGRA SIEYYVGQVM RNNESTETGY VIKVFNNGIV VLVPKFGVEG LIRLDNLTED PNSAAFDEVE Y KLTFVPTN SDKPRDVYVF DKVEVQVRSV MDPITSKRKA ELLLK

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Macromolecule #12: Exosome complex exonuclease RRP6

MacromoleculeName: Exosome complex exonuclease RRP6 / type: protein_or_peptide / ID: 12 / Details: Inactive point mutant D296N / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 84.159586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI DEHHESFELK EEDISDLWNN FGNIMDNLL EMSDHSLDKL NCAINSKSRG SDLQYLGEFS GKNFSPTKRV EKPQLKFKSP IDNSESHPFI PLLKEKPNAL K PLSESLRL ...String:
MTSENPDVLL SRVINVVRAA SSLASQDVDF YKNLDRGFSK DLKSKADKLA DMANEIILSI DEHHESFELK EEDISDLWNN FGNIMDNLL EMSDHSLDKL NCAINSKSRG SDLQYLGEFS GKNFSPTKRV EKPQLKFKSP IDNSESHPFI PLLKEKPNAL K PLSESLRL VDDDENNPSH YPHPYEYEID HQEYSPEILQ IREEIPSKSW DDSVPIWVDT STELESMLED LKNTKEIAVD LE HHDYRSY YGIVCLMQIS TRERDYLVDT LKLRENLHIL NEVFTNPSIV KVFHGAFMNI IWLQRDLGLY VVGLFDTYHA SKA IGLPRH SLAYLLENFA NFKTSKKYQL ADWRIRPLSK PMTAYARADT HFLLNIYDQL RNKLIESNKL AGVLYESRNV AKRR FEYSK YRPLTPSSEV YSPIEKESPW KILMYQYNIP PEREVLVREL YQWRDLIARR DDESPRFVMP NQLLAALVAY TPTDV IGVV SLTNGVTEHV RQNAKLLANL IRDALRNIKN TNEEATPIPS SETKADGILL ETISVPQIRD VMERFSVLCN SNISKS RAK PVTNSSILLG KILPREEHDI AYSKDGLPNK VKTEDIRIRA QNFKSALANL EDIIFEIEKP LVVPVKLEEI KTVDPAS AP NHSPEIDNLD DLVVLKKKNI QKKQPAKEKG VTEKDAVDYS KIPNILSNKP GQNNRQQKKR RFDPSSSDSN GPRAAKKR R PAAKGKNLSF KR

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Macromolecule #13: Exosome complex protein LRP1

MacromoleculeName: Exosome complex protein LRP1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 21.086297 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MEDIEKIKPY VRSFSKALDE LKPEIEKLTS KSLDEQLLLL SDERAKLELI NRYAYVLSSL MFANMKVLGV KDMSPILGEL KRVKSYMDK AKQYDNRITK SNEKSQAEQE KAKNIISNVL DGNKNQFEPS ISRSNFQGKH TKFENDELAE STTTKIIDST D HIRKASSK KSKRLDKVGK KKGGKK

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Macromolecule #14: ATP-dependent RNA helicase DOB1

MacromoleculeName: ATP-dependent RNA helicase DOB1 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: RNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 122.260094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDSTDLFDVF EETPVELPTD SNGEKNADTN VGDTPDHTQD KKHGLEEEKE EHEENNSENK KIKSNKSKTE DKNKKVVVPM LADSFEQEA SREVDASKGL TNSETLQVEQ DGKVRLSHQV RHQVALPPNY DYTPIAEHKR VNEARTYPFT LDPFQDTAIS C IDRGESVL ...String:
MDSTDLFDVF EETPVELPTD SNGEKNADTN VGDTPDHTQD KKHGLEEEKE EHEENNSENK KIKSNKSKTE DKNKKVVVPM LADSFEQEA SREVDASKGL TNSETLQVEQ DGKVRLSHQV RHQVALPPNY DYTPIAEHKR VNEARTYPFT LDPFQDTAIS C IDRGESVL VSAHTSAGKT VVAEYAIAQS LKNKQRVIYT SPIKALSNQK YRELLAEFGD VGLMTGDITI NPDAGCLVMT TE ILRSMLY RGSEVMREVA WVIFDEVHYM RDKERGVVWE ETIILLPDKV RYVFLSATIP NAMEFAEWIC KIHSQPCHIV YTN FRPTPL QHYLFPAHGD GIYLVVDEKS TFREENFQKA MASISNQIGD DPNSTDSRGK KGQTYKGGSA KGDAKGDIYK IVKM IWKKK YNPVIVFSFS KRDCEELALK MSKLDFNSDD EKEALTKIFN NAIALLPETD RELPQIKHIL PLLRRGIGIH HSGLL PILK EVIEILFQEG FLKVLFATET FSIGLNMPAK TVVFTSVRKW DGQQFRWVSG GEYIQMSGRA GRRGLDDRGI VIMMID EKM EPQVAKGMVK GQADRLDSAF HLGYNMILNL MRVEGISPEF MLEHSFFQFQ NVISVPVMEK KLAELKKDFD GIEVEDE EN VKEYHEIEQA IKGYREDVRQ VVTHPANALS FLQPGRLVEI SVNGKDNYGW GAVVDFAKRI NKRNPSAVYT DHESYIVN V VVNTMYIDSP VNLLKPFNPT LPEGIRPAEE GEKSICAVIP ITLDSIKSIG NLRLYMPKDI RASGQKETVG KSLREVNRR FPDGIPVLDP VKNMKIEDED FLKLMKKIDV LNTKLSSNPL TNSMRLEELY GKYSRKHDLH EDMKQLKRKI SESQAVIQLD DLRRRKRVL RRLGFCTPND IIELKGRVAC EISSGDELLL TELIFNGNFN ELKPEQAAAL LSCFAFQERC KEAPRLKPEL A EPLKAMRE IAAKIAKIMK DSKIEVVEKD YVESFRHELM EVVYEWCRGA TFTQICKMTD VYEGSLIRMF KRLEELVKEL VD VANTIGN SSLKEKMEAV LKLIHRDIVS AGSLYL

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Macromolecule #15: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog...

MacromoleculeName: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
type: protein_or_peptide / ID: 15
Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs ...Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 4.101711 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)PNLIISNVG YSELRKPEGV ISGRKT FGD N

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.4 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22439

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