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- PDB-5jea: Structure of a cytoplasmic 11-subunit RNA exosome complex includi... -

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Basic information

Entry
Database: PDB / ID: 5jea
TitleStructure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA
Components
  • (Exosome complex component ...) x 9
  • Exosome complex exonuclease DIS3
  • RNA (29-MER)
  • Superkiller protein 7,Endolysin
KeywordsHYDROLASE/RNA / exosome / Ski7 / nuclease / RNA degradation / hydrolase- RNA complex / HYDROLASE-RNA complex
Function / homology
Function and homology information


Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) ...Eukaryotic Translation Elongation / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / HSF1 activation / rRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / Protein methylation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / translational elongation / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / RNA processing / translation elongation factor activity / RNA endonuclease activity / viral release from host cell by cytolysis / Neutrophil degranulation / peptidoglycan catabolic process / protein catabolic process / mRNA processing / protein-macromolecule adaptor activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / host cell cytoplasm / tRNA binding / defense response to bacterium / translation / GTPase activity / protein-containing complex binding / GTP binding / nucleolus / mitochondrion / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 domain / RRP4, S1 domain / Exosome complex component RRP45 / Rrp40, S1 domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #700 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex exonuclease RRP44, S1 domain / S1 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 / PIN domain / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / GHMP Kinase, N-terminal domain / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / K Homology domain, type 1 / 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 / Large family of predicted nucleotide-binding domains / PIN domain / K Homology domain, type 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / PIN-like domain superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Endolysin T4 type / T4-type lysozyme / Ribosomal protein S1-like RNA-binding domain / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Endolysin / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 ...RNA / RNA (> 10) / Endolysin / Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex exonuclease DIS3 / Exosome complex component RRP40 / Superkiller protein 7 / Exosome complex component RRP42
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Enterobacteria phage T4 (virus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKowalinski, E. / Ebert, J. / Stegmann, E. / Conti, E.
Funding support Germany, 6items
OrganizationGrant numberCountry
European Research Council294371 Germany
German Research FoundationSFB646 Germany
German Research FoundationSFB1035 Germany
German Research FoundationGRK1721 Germany
German Research FoundationFOR1680 Germany
German Research FoundationCIPSM Germany
CitationJournal: Mol.Cell / Year: 2016
Title: Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.
Authors: Kowalinski, E. / Kogel, A. / Ebert, J. / Reichelt, P. / Stegmann, E. / Habermann, B. / Conti, E.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Atomic model / Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / ndb_struct_na_base_pair / pdbx_audit_support / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _ndb_struct_na_base_pair.hbond_type_28 / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exosome complex component RRP45
B: Exosome complex component SKI6
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: Exosome complex exonuclease DIS3
K: Superkiller protein 7,Endolysin
R: RNA (29-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)442,28124
Polymers441,29612
Non-polymers98512
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54920 Å2
ΔGint-359 kcal/mol
Surface area141180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.080, 182.530, 250.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Exosome complex component ... , 9 types, 9 molecules ABCDEFGHI

#1: Protein Exosome complex component RRP45 / / Ribosomal RNA-processing protein 45


Mass: 34001.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636
#2: Protein Exosome complex component SKI6 / / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27892.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948
#3: Protein Exosome complex component RRP43 / / Ribosomal RNA-processing protein 43


Mass: 44109.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359
#4: Protein Exosome complex component RRP46 / / Ribosomal RNA-processing protein 46


Mass: 24659.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Production host: Escherichia coli (E. coli) / References: UniProt: P53256
#5: Protein Exosome complex component RRP42 / / Ribosomal RNA-processing protein 42


Mass: 29391.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277
#6: Protein Exosome complex component MTR3 / / mRNA transport regulator 3


Mass: 27573.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240
#7: Protein Exosome complex component RRP40 / / Ribosomal RNA-processing protein 40


Mass: 26939.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285
#8: Protein Exosome complex component RRP4 / / Ribosomal RNA-processing protein 4


Mass: 34603.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792
#9: Protein Exosome complex component CSL4 / / CEP1 synthetic lethal protein 4


Mass: 31911.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859

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Protein , 2 types, 2 molecules JK

#10: Protein Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 114212.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#11: Protein Superkiller protein 7,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 31666.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: ATCC 204508 / S288c / Gene: SKI7, YOR076C, YOR29-27 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08491, UniProt: P00720, lysozyme

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RNA chain , 1 types, 1 molecules R

#12: RNA chain RNA (29-MER)


Mass: 14336.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 146 molecules

#13: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#14: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#15: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 27 % 2-Methyl-2,4-pentanediol (MPD), 0.1 M 2-(N-morpholino)ethanesulfonic acid (MES) pH 6 and 10 mM CaCl2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.65→66.69 Å / Num. obs: 272923 / % possible obs: 100 % / Redundancy: 10.26 % / CC1/2: 0.99 / Rmerge(I) obs: 0.211 / Net I/σ(I): 7.33
Reflection shellResolution: 2.65→2.75 Å / Redundancy: 8.16 % / Rmerge(I) obs: 1.762 / Mean I/σ(I) obs: 1.14 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IFD

4ifd


Resolution: 2.65→66.688 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 27.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2586 13635 5 %
Rwork0.2152 --
obs0.2174 272892 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→66.688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26423 524 61 134 27142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427484
X-RAY DIFFRACTIONf_angle_d0.76637349
X-RAY DIFFRACTIONf_dihedral_angle_d14.1710261
X-RAY DIFFRACTIONf_chiral_restr0.0294390
X-RAY DIFFRACTIONf_plane_restr0.0034726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.68010.36444500.3398592X-RAY DIFFRACTION100
2.6801-2.71160.37414530.33858683X-RAY DIFFRACTION100
2.7116-2.74470.34974460.32468582X-RAY DIFFRACTION100
2.7447-2.77950.37694590.32348711X-RAY DIFFRACTION100
2.7795-2.8160.32644530.30428579X-RAY DIFFRACTION100
2.816-2.85460.33524630.28888706X-RAY DIFFRACTION100
2.8546-2.89540.31974520.28068588X-RAY DIFFRACTION100
2.8954-2.93860.31764540.28248677X-RAY DIFFRACTION100
2.9386-2.98450.3134560.27838619X-RAY DIFFRACTION100
2.9845-3.03350.28574580.27238687X-RAY DIFFRACTION100
3.0335-3.08580.29494550.27298586X-RAY DIFFRACTION100
3.0858-3.14190.31084580.27168647X-RAY DIFFRACTION100
3.1419-3.20230.34954520.26828697X-RAY DIFFRACTION100
3.2023-3.26770.30684500.25048580X-RAY DIFFRACTION100
3.2677-3.33870.28584610.23618684X-RAY DIFFRACTION100
3.3387-3.41640.30114490.23838680X-RAY DIFFRACTION100
3.4164-3.50180.28654530.23418593X-RAY DIFFRACTION100
3.5018-3.59650.30754570.23228626X-RAY DIFFRACTION100
3.5965-3.70230.26894540.21818665X-RAY DIFFRACTION100
3.7023-3.82180.24524550.20568634X-RAY DIFFRACTION100
3.8218-3.95840.23624510.19388699X-RAY DIFFRACTION100
3.9584-4.11690.2484590.20058586X-RAY DIFFRACTION100
4.1169-4.30420.23324600.18348658X-RAY DIFFRACTION100
4.3042-4.53110.21314530.17728648X-RAY DIFFRACTION100
4.5311-4.81490.20594630.16658677X-RAY DIFFRACTION100
4.8149-5.18650.23674510.18148588X-RAY DIFFRACTION100
5.1865-5.70820.27864490.20438675X-RAY DIFFRACTION100
5.7082-6.53360.23584520.21058647X-RAY DIFFRACTION100
6.5336-8.22920.22114540.18858651X-RAY DIFFRACTION100
8.2292-66.70950.20964550.18488612X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.3316 Å / Origin y: -12.6773 Å / Origin z: -32.9798 Å
111213212223313233
T0.5175 Å2-0.0012 Å2-0.0022 Å2-0.5953 Å20.0223 Å2--0.4783 Å2
L0.3477 °2-0.029 °2-0.0557 °2-0.5929 °2-0.0299 °2--0.278 °2
S0.0194 Å °0.0864 Å °-0.0191 Å °-0.0303 Å °-0.0029 Å °0.0526 Å °-0.0691 Å °-0.0443 Å °0 Å °
Refinement TLS groupSelection details: all

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