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- PDB-8r1o: Structure of C. thermophilum RNA exosome core -

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Basic information

Entry
Database: PDB / ID: 8r1o
TitleStructure of C. thermophilum RNA exosome core
Components
  • (Exoribonuclease phosphorolytic domain-containing ...) x 3
  • (Putative exosome ...) x 2
  • Exoribonuclease-like protein
  • Exosome complex component MTR3
  • Ribosomal RNA-processing protein 40
  • Rrp45
KeywordsRNA BINDING PROTEIN / nuclease / RNA degradation / RNA metabolism / RNA binding
Function / homology
Function and homology information


CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / 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) ...CUT catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / 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) / nuclear mRNA surveillance / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / RNA processing / rRNA processing / nucleolus / RNA binding / cytoplasm
Similarity search - Function
Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal 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 Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal 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 / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / : / : / 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 / K Homology domain, type 1 / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Ribosomal RNA-processing protein 42 / Ribosomal RNA-processing protein 40 / Ribosomal RNA-processing protein 43 / Exosome complex component RRP45 / Putative exosome complex protein / Uncharacterized protein / Exoribonuclease phosphorolytic domain-containing protein / Putative exosome 3'->5 protein / Exosome complex component MTR3
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsLazzaretti, D. / Liebau, J. / Pilsl, M. / Sprangers, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SP 1324/3-1 Germany
Citation
Journal: Nat Commun / Year: 2025
Title: 4D structural biology-quantitative dynamics in the eukaryotic RNA exosome complex.
Authors: Jobst Liebau / Daniela Lazzaretti / Torben Fürtges / Anna Bichler / Michael Pilsl / Till Rudack / Remco Sprangers /
Abstract: Molecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR ...Molecular machines play pivotal roles in all biological processes. Most structural methods, however, are unable to directly probe molecular motions. Here, we demonstrate that dedicated NMR experiments can provide quantitative insights into functionally important dynamic regions in very large asymmetric protein complexes. We establish this for the 410 kDa eukaryotic RNA exosome complex that contains ten distinct protein chains. Methyl-group and fluorine NMR experiments reveal site-specific interactions among subunits and with an RNA substrate. Furthermore, we extract quantitative insights into conformational changes within the complex in response to substrate and subunit binding for regions that are invisible in static cryo-EM and crystal structures. In particular, we identify a flexible plug region that can block an aberrant route for RNA towards the active site. Based on molecular dynamics simulations and NMR data, we provide a model that shows how the flexible plug is structured in the open and closed conformations. Our work thus demonstrates that a combination of state-of-the-art structural biology methods can provide quantitative insights into large molecular machines that go significantly beyond the well-resolved and static images of biomolecular complexes, thereby adding the time domain to structural biology.
#1: Journal: Biorxiv / Year: 2024
Title: Beyond static structures: quantitative dynamics in the eukaryotic RNA exosome complex
Authors: Liebau, J. / Lazzaretti, D. / Bichler, A. / Pilsl, M. / Sprangers, R.
History
DepositionNov 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rrp45
B: Exoribonuclease phosphorolytic domain-containing protein
C: Exoribonuclease-like protein
D: Exoribonuclease phosphorolytic domain-containing protein
E: Exoribonuclease phosphorolytic domain-containing protein
F: Exosome complex component MTR3
G: Ribosomal RNA-processing protein 40
H: Putative exosome complex protein
I: Putative exosome 3'->5 protein


Theoretical massNumber of molelcules
Total (without water)294,7269
Polymers294,7269
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 4 molecules ACFG

#1: Protein Rrp45


Mass: 32470.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0027490 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S755
#3: Protein Exoribonuclease-like protein


Mass: 39553.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0014300 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S1P1
#6: Protein Exosome complex component MTR3 / mRNA transport regulator 3


Mass: 30541.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: MTR3, CTHT_0115690 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CT46
#7: Protein Ribosomal RNA-processing protein 40


Mass: 27955.145 Da / Num. of mol.: 1 / Mutation: G-1, A0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0008000 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZX8

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Exoribonuclease phosphorolytic domain-containing ... , 3 types, 3 molecules BDE

#2: Protein Exoribonuclease phosphorolytic domain-containing protein


Mass: 29986.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0055610 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SC21
#4: Protein Exoribonuclease phosphorolytic domain-containing protein


Mass: 27979.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0056790 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCD1
#5: Protein Exoribonuclease phosphorolytic domain-containing protein


Mass: 43949.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0002870 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZG4

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Putative exosome ... , 2 types, 2 molecules HI

#8: Protein Putative exosome complex protein


Mass: 38403.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0045080 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S9A0
#9: Protein Putative exosome 3'->5 protein


Mass: 23886.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Gene: CTHT_0062250 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SE33

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Details

Has protein modificationN

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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

ComponentName: RNA exosome core (Exo9) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.294 MDa / Experimental value: NO
Source (natural)Organism: Thermochaetoides thermophila DSM 1495 (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-CodonPlus
Buffer solutionpH: 7.5
Details: 20 mM Na-Phosphate buffer pH 7.5, 300 mM NaCl, 1 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
14 mMSodium phosphate (monobasic)NaH2PO41
216 mMSodium phosphate (dibasic)Na2HPO41
3300 mMSodium chlorideNaCl1
41 mMDithiothreitolC4H10O2S21
SpecimenConc.: 0.53 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample frozen directly after S200 size exclusion column
Specimen supportDetails: Grids were glow discharged twice at 15 mA, 0.39 mBar, for 100 seconds each time
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Sample volume 3 ul Wait time 5 s, Blot time 5 s, Delay time 0 s Force 12

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 6.5 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6579
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2SerialEMimage acquisition
4RELION4.0.1CTF correction
5CTFFIND4.1CTF correction
8UCSF ChimeraX1.1model fitting
9PHENIX1.20.1-4487model fitting
11PHENIX1.20.1-4487model refinement
12ISOLDE1.6model refinement
13Coot0.9.6model refinement
14RELION4.0.1initial Euler assignment
15RELION4.0.1final Euler assignment
16RELION4.0.1classification
17RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2448810
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276958 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model building
ID 3D fitting-IDDetailsSource nameTypeAccession codeInitial refinement model-ID
11multi-template models built using structures of homolog proteinsModellerin silico model
21AlphaFoldin silico modelAF-G0S755-F1,AF-G0SC21-F1,AF-G0S1P1-F1,AF-G0SCD1-F1,AF-G0RZG4-F1,AF-P0CT46-F1,AF-G0RZX8-F1,AF-G0S9A0-F1,AF-G0SE33-F12
RefinementCross valid method: NONE

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