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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


CUT catabolic process / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / 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 / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / 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)
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
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
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details

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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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Details

Has protein modificationN

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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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