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- PDB-6h25: Human nuclear RNA exosome EXO-10-MPP6 complex -

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Basic information

Entry
Database: PDB / ID: 6h25
TitleHuman nuclear RNA exosome EXO-10-MPP6 complex
Components
  • (Exosome complex component ...) x 9
  • Exosome complex exonuclease RRP44
  • M-phase phosphoprotein 6
  • U44 ssRNA
KeywordsRNA BINDING PROTEIN / nuclear exosome / RNA decay / cryoEM / hEXO-10 / hDIS3 / hMPP6
Function / homology
Function and homology information


DNA deamination / nucleolar exosome (RNase complex) / mRNA decay by 3' to 5' exoribonuclease / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process ...DNA deamination / nucleolar exosome (RNase complex) / mRNA decay by 3' to 5' exoribonuclease / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / 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 / histone mRNA catabolic process / nuclear mRNA surveillance / positive regulation of isotype switching / mRNA 3'-UTR AU-rich region binding / 7S RNA binding / isotype switching / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process / 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 / guanyl-nucleotide exchange factor activity / euchromatin / fibrillar center / rRNA processing / chromosome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / positive regulation of cell growth / endonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / immune response / intracellular membrane-bounded organelle / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein 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 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 / : / 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) / GHMP Kinase, N-terminal domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / 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 / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Ribosomal Protein S5; domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 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 ...RNA / RNA (> 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGerlach, P. / Schuller, J.M. / Falk, S. / Basquin, J. / Conti, E.
Funding support5items
OrganizationGrant numberCountry
European Molecular Biology OrganizationALTF 1008-2015
European CommissionERC-2016-ADG 740329 EXORICO
German Research FoundationSFB646, SFB1035, GRK1721
Louis-Jeantet Foundation
Max Planck Society
CitationJournal: Elife / Year: 2018
Title: Distinct and evolutionary conserved structural features of the human nuclear exosome complex.
Authors: Piotr Gerlach / Jan M Schuller / Fabien Bonneau / Jérôme Basquin / Peter Reichelt / Sebastian Falk / Elena Conti /
Abstract: The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to ...The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes.
History
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.2May 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
A: Exosome complex component RRP45
B: Exosome complex component RRP41
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: Exosome complex exonuclease RRP44
K: M-phase phosphoprotein 6
R: U44 ssRNA


Theoretical massNumber of molelcules
Total (without water)421,24912
Polymers421,24912
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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

#1: Protein Exosome complex component RRP45 / / Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome- ...Autoantigen PM/Scl 1 / Exosome component 9 / P75 polymyositis-scleroderma overlap syndrome-associated autoantigen / Polymyositis/scleroderma autoantigen 1 / Polymyositis/scleroderma autoantigen 75 kDa / PM/Scl-75


Mass: 49370.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC9, PMSCL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06265
#2: Protein Exosome complex component RRP41 / / Exosome component 4 / Ribosomal RNA-processing protein 41 / p12A


Mass: 26773.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC4, RRP41, SKI6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NPD3
#3: Protein Exosome complex component RRP43 / / Exosome component 8 / Opa-interacting protein 2 / OIP-2 / Ribosomal RNA-processing protein 43 / p9


Mass: 30317.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC8, OIP2, RRP43 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96B26
#4: Protein Exosome complex component RRP46 / / Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing ...Chronic myelogenous leukemia tumor antigen 28 / Exosome component 5 / Ribosomal RNA-processing protein 46 / p12B


Mass: 25524.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC5, CML28, RRP46 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT4
#5: Protein Exosome complex component RRP42 / / Exosome component 7 / Ribosomal RNA-processing protein 42 / p8


Mass: 32216.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC7, KIAA0116, RRP42 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15024
#6: Protein Exosome complex component MTR3 / / Exosome component 6 / mRNA transport regulator 3 homolog / hMtr3 / p11


Mass: 28623.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC6, MTR3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5RKV6
#7: Protein Exosome complex component RRP40 / / Exosome component 3 / Ribosomal RNA-processing protein 40 / p10


Mass: 30906.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC3, RRP40, CGI-102 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NQT5
#8: Protein Exosome complex component RRP4 / / Exosome component 2 / Ribosomal RNA-processing protein 4


Mass: 33190.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC2, RRP4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13868
#9: Protein Exosome complex component CSL4 / / Exosome component 1


Mass: 21835.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOSC1, CSL4, CGI-108 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3B2

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Protein , 2 types, 2 molecules JK

#10: Protein Exosome complex exonuclease RRP44 / Protein DIS3 homolog / Ribosomal RNA-processing protein 44


Mass: 109522.227 Da / Num. of mol.: 1 / Mutation: D146N, D487N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIS3, KIAA1008, RRP44 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2L1, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#11: Protein M-phase phosphoprotein 6


Mass: 19542.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH6, MPP6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99547

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RNA chain , 1 types, 1 molecules R

#12: RNA chain U44 ssRNA


Mass: 13426.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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
1Human nuclear RNA exosome EXO-14 complexCOMPLEXall0MULTIPLE SOURCES
2exosome complexCOMPLEX#1-#111RECOMBINANT
3U44 ssRNACOMPLEX#121RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHepes1
2150 mMNaClSodium chloride1
32 mMDTT1
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 FIELDBright-field microscopy
Image recordingElectron dose: 47 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 8047

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2396236
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110958 / Symmetry type: POINT
RefinementHighest resolution: 3.8 Å

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