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

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Basic information

Entry
Database: PDB / ID: 8pel
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


TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing ...TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.81 Å
AuthorsLazzaretti, D. / Holdermann, I. / 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
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 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: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33600 Å2
ΔGint-149 kcal/mol
Surface area95640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.525, 148.385, 195.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium Sulphate 0.1M Sodium Acetate pH 5.5 10% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 3.81→48.9 Å / Num. obs: 29143 / % possible obs: 99.57 % / Redundancy: 13.5 % / Biso Wilson estimate: 74.733 Å2 / CC1/2: 0.984 / CC star: 0.996 / Net I/σ(I): 5.01
Reflection shellResolution: 3.81→3.946 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1.19 / Num. unique obs: 2793 / CC1/2: 0.586 / CC star: 0.86 / % possible all: 97.14

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Processing

Software
NameVersionClassification
XDSJan 10, 2022data reduction
XSCALEJan 10, 2022data scaling
Coot0.9.6model building
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
ISOLDEv1.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.81→48.9 Å / SU ML: 0.6154 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2925 1454 5 %Random selection
Rwork0.2432 27670 --
obs0.2456 29114 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.52 Å2
Refinement stepCycle: LAST / Resolution: 3.81→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17656 0 0 0 17656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004217980
X-RAY DIFFRACTIONf_angle_d0.69224444
X-RAY DIFFRACTIONf_chiral_restr0.04522871
X-RAY DIFFRACTIONf_plane_restr0.00443162
X-RAY DIFFRACTIONf_dihedral_angle_d5.81832491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.81-3.940.3881370.35462591X-RAY DIFFRACTION94.82
3.94-4.10.32051430.29182729X-RAY DIFFRACTION99.9
4.1-4.290.31961450.26432759X-RAY DIFFRACTION99.97
4.29-4.510.2971450.24352735X-RAY DIFFRACTION99.93
4.51-4.80.30531440.23132772X-RAY DIFFRACTION99.86
4.8-5.170.2571440.22062734X-RAY DIFFRACTION99.9
5.17-5.680.30031460.24692777X-RAY DIFFRACTION100
5.68-6.50.30761470.26842803X-RAY DIFFRACTION100
6.51-8.190.27781490.23432822X-RAY DIFFRACTION100
8.19-48.90.25971550.20452948X-RAY DIFFRACTION99.61

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