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- PDB-6fsz: Structure of the nuclear RNA exosome -

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Entry
Database: PDB / ID: 6fsz
TitleStructure of the nuclear RNA exosome
Components
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • ATP-dependent RNA helicase DOB1
  • Exosome complex protein LRP1
  • M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
  • 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')
KeywordsRNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase
Function / homology
Function and homology information


nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear mRNA surveillance of mRNA 3'-end processing / regulatory ncRNA 3'-end processing / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / CUT catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / exosome (RNase complex) / cytoplasmic exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / 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) / 3'-5' RNA helicase activity / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / poly(A) binding / mRNA 3'-UTR AU-rich region binding / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / regulation of telomere maintenance / poly(U) RNA binding / maturation of 5.8S rRNA / nonfunctional rRNA decay / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / enzyme regulator activity / RNA endonuclease activity / mRNA processing / double-stranded RNA binding / manganese ion binding / regulation of gene expression / double-stranded DNA binding / endonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / oxidoreductase activity / tRNA binding / RNA helicase activity / single-stranded RNA binding / 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 / : / 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 / PIN domain / Exosome complex component RRP45 ...Exosome-associated factor Rrp47/DNA strand repair C1D / 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 / PIN domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Exosome-associated factor Rrp6, N-terminal / Exosome complex exonuclease Rrp6-like / : / PMC2NT (NUC016) domain / : / rRNA-processing arch domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Mtr4-like, beta-barrel domain / : / Ribonuclease II/R / RNB domain / RNB / : / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / 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 / HRDC domain superfamily / Large family of predicted nucleotide-binding domains / 3'-5' exonuclease / Prismane-like superfamily / 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 domain / DEAD/DEAH box helicase / 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
RNA / RNA (> 10) / 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 ...RNA / RNA (> 10) / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSchuller, J.M. / Falk, S. / Conti, E.
Funding support Belgium, 1items
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Other / Source and taxonomy / Category: atom_sites / entity_src_gen
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 1.4Dec 18, 2019Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
2: 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')
AA: Exosome complex component RRP45
BB: Exosome complex component SKI6
CC: Exosome complex component RRP43
DD: Exosome complex component RRP46
EE: Exosome complex component RRP42
FF: Exosome complex component MTR3
GG: Exosome complex component RRP40
HH: Exosome complex component RRP4
II: Exosome complex component CSL4
JJ: Exosome complex exonuclease DIS3
KK: Exosome complex exonuclease RRP6
LL: Exosome complex protein LRP1
MM: ATP-dependent RNA helicase DOB1
NN: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog


Theoretical massNumber of molelcules
Total (without water)641,38915
Polymers641,38915
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#2: Protein Exosome complex component RRP45 / Ribosomal RNA-processing protein 45


Mass: 33799.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636
#3: Protein Exosome complex component SKI6 / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27794.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948
#4: Protein Exosome complex component RRP43 / Ribosomal RNA-processing protein 43


Mass: 43977.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359
#5: Protein Exosome complex component RRP46 / Ribosomal RNA-processing protein 46


Mass: 26913.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Production host: Escherichia coli (E. coli) / References: UniProt: P53256
#6: Protein Exosome complex component RRP42 / Ribosomal RNA-processing protein 42


Mass: 29294.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277
#7: Protein Exosome complex component MTR3 / mRNA transport regulator 3


Mass: 27559.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240
#8: Protein Exosome complex component RRP40 / Ribosomal RNA-processing protein 40


Mass: 26778.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285
#9: Protein Exosome complex component RRP4 / Ribosomal RNA-processing protein 4


Mass: 39714.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792
#10: Protein Exosome complex component CSL4 / CEP1 synthetic lethal protein 4


Mass: 32805.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859

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Exosome complex exonuclease ... , 2 types, 2 molecules JJKK

#11: Protein Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 113983.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#12: Protein Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 84159.586 Da / Num. of mol.: 1 / Mutation: D296N
Source method: isolated from a genetically manipulated source
Details: Inactive point mutant D296N
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Protein , 2 types, 2 molecules LLMM

#13: Protein Exosome complex protein LRP1 / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801
#14: Protein ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 122260.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase

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RNA chain / Protein/peptide , 2 types, 2 molecules 2NN

#15: Protein/peptide M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog / Exosome-associated RNA-binding protein MPP6


Mass: 4101.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MPP6, YNR024W, N3230 / Production host: Escherichia coli (E. coli) / References: UniProt: P53725
#1: RNA chain 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')


Mass: 7158.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Nuclear RNA exosomeCOMPLEXall0MULTIPLE SOURCES
2Nuclear RNA exosomeCOMPLEX#2-#151RECOMBINANT
3nucleic acidCOMPLEX#11NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Saccharomyces cerevisiae (brewer's yeast)4932
33Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22439 / Symmetry type: POINT

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