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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


nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing ...nuclear polyadenylation-dependent mRNA catabolic process / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / 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 / RNA processing / rRNA processing / nucleolus / RNA binding / cytoplasm
Similarity search - Function
Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal 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 complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal 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 / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / : / : / 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 / Uncharacterized protein / 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
CitationJournal: 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

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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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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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