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- PDB-8xie: Archaeal exosome complex (Rrp4-Rrp41-Rrp42) -

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Basic information

Entry
Database: PDB / ID: 8xie
TitleArchaeal exosome complex (Rrp4-Rrp41-Rrp42)
Components
  • Exosome complex component Rrp4
  • Exosome complex component Rrp41
  • Exosome complex component Rrp42
KeywordsHYDROLASE / archaeal exosome complex
Function / homology
Function and homology information


intracellular organelle / exosome (RNase complex) / cytoplasmic exosome (RNase complex) / rRNA catabolic process / poly(A) binding / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / RNA binding / cytoplasm
Similarity search - Function
Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / RRP4, S1 domain / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / : / : / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 ...Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / RRP4, S1 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 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / K Homology domain / K homology RNA-binding domain / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Rrp4
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKim, H.S. / Park, S.H. / Kim, S.H. / Hwang, K.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biomolecules / Year: 2024
Title: Structural Insights into the Rrp4 Subunit from the Crystal Structure of the Thermoplasma acidophilum Exosome.
Authors: Park, S. / Kim, H.S. / Bang, K. / Han, A. / Shin, B. / Seo, M. / Kim, S. / Hwang, K.Y.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exosome complex component Rrp41
B: Exosome complex component Rrp42
C: Exosome complex component Rrp41
D: Exosome complex component Rrp41
E: Exosome complex component Rrp42
F: Exosome complex component Rrp42
G: Exosome complex component Rrp4
I: Exosome complex component Rrp4
H: Exosome complex component Rrp4


Theoretical massNumber of molelcules
Total (without water)247,3529
Polymers247,3529
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27290 Å2
ΔGint-138 kcal/mol
Surface area84240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.822, 240.822, 216.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Exosome complex component Rrp41


Mass: 27557.555 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Gene: rrp41, Ta1293 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9HIP2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein Exosome complex component Rrp42


Mass: 28395.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Gene: rrp42, Ta1294 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HIP1
#3: Protein Exosome complex component Rrp4


Mass: 26497.498 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (acidophilic)
Gene: rrp4, Ta1292 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HIP3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 7.34 Å3/Da / Density % sol: 83.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: sodium acetate trihydrate, ammonium sulfate, 20% glycerol, pH 4.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 86230 / % possible obs: 94.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 5.3
Reflection shellResolution: 3.5→3.6 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / Num. unique obs: 86210

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Processing

Software
NameVersionClassification
PHENIX(1.20_4459: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→49.43 Å / SU ML: 0.57 / Cross valid method: NONE / σ(F): 1.45 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1986 2.3 %
Rwork0.2285 --
obs0.2295 86202 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16049 0 0 134 16183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d7.0832218
X-RAY DIFFRACTIONf_chiral_restr0.0952504
X-RAY DIFFRACTIONf_plane_restr0.0172851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.38071240.3535086X-RAY DIFFRACTION81
3.59-3.690.3581350.34135659X-RAY DIFFRACTION90
3.69-3.80.35291350.32735699X-RAY DIFFRACTION90
3.8-3.920.39331380.3125788X-RAY DIFFRACTION91
3.92-4.060.31891340.29325885X-RAY DIFFRACTION93
4.06-4.220.33031420.26375979X-RAY DIFFRACTION94
4.22-4.410.2681410.22726065X-RAY DIFFRACTION96
4.41-4.640.23291440.20656111X-RAY DIFFRACTION96
4.64-4.940.24031500.18676177X-RAY DIFFRACTION97
4.94-5.320.2251460.19456239X-RAY DIFFRACTION98
5.32-5.850.27611410.19736264X-RAY DIFFRACTION98
5.85-6.70.25051540.20636313X-RAY DIFFRACTION98
6.7-8.430.2031480.16626370X-RAY DIFFRACTION99

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