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- PDB-2jea: Structure of a 9-subunit archaeal exosome bound to RNA -

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Basic information

Entry
Database: PDB / ID: 2jea
TitleStructure of a 9-subunit archaeal exosome bound to RNA
Components
  • (EXOSOME COMPLEX EXONUCLEASE ...) x 2
  • EXOSOME COMPLEX RNA-BINDING PROTEIN 1
  • RNA
KeywordsHYDROLASE/RNA / HYDROLASE RNA COMPLEX / HYDROLASE-RNA COMPLEX / NUCLEASE / HYDROLASE / RNA-BINDING / EXONUCLEASE / PHOSPHOROLYTIC / EXORIBONUCLEASE / RNA DEGRADATION / RRP4 / RRP42 / RRP41 / EXOSOME / RNASE PH
Function / homology
Function and homology information


CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / U4 snRNA 3'-end processing / 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) / rRNA catabolic process / poly(A) binding / mRNA 3'-UTR AU-rich region binding / RNA catabolic process ...CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / U4 snRNA 3'-end processing / 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) / 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 / gene expression / RNA binding / cytoplasm
Similarity search - Function
: / Exosome RNA binding protein RRP4 N-terminal domain / Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / GHMP Kinase, N-terminal domain / : ...: / Exosome RNA binding protein RRP4 N-terminal domain / Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / GHMP Kinase, N-terminal domain / : / : / 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 / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / S1 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Rrp4
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLorentzen, E. / Conti, E.
CitationJournal: Embo Rep. / Year: 2007
Title: RNA Channelling by the Archaeal Exosome.
Authors: Lorentzen, E. / Dziembowski, A. / Lindner, D. / Seraphin, B. / Conti, E.
History
DepositionJan 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "IC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: RNA
I: EXOSOME COMPLEX RNA-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0805
Polymers97,8414
Non-polymers2381
Water2,198122
1
A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: RNA
I: EXOSOME COMPLEX RNA-BINDING PROTEIN 1
hetero molecules

A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: RNA
I: EXOSOME COMPLEX RNA-BINDING PROTEIN 1
hetero molecules

A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
C: RNA
I: EXOSOME COMPLEX RNA-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,23915
Polymers293,52412
Non-polymers7153
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,z+1/2,-x-1/21
crystal symmetry operation7_454-z-1/2,-x,y-1/21
Buried area30590 Å2
ΔGint-155.5 kcal/mol
Surface area79480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.850, 135.850, 135.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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EXOSOME COMPLEX EXONUCLEASE ... , 2 types, 2 molecules AB

#1: Protein EXOSOME COMPLEX EXONUCLEASE 2 / EXOSOME COMPLEX OF RRP41 / RRP42 AND RRP4


Mass: 30422.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC0, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Protein EXOSOME COMPLEX EXONUCLEASE 1


Mass: 27764.125 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UXC2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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RNA chain / Protein , 2 types, 2 molecules CI

#3: RNA chain RNA


Mass: 11429.052 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Protein EXOSOME COMPLEX RNA-BINDING PROTEIN 1


Mass: 28225.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UXC4

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Non-polymers , 2 types, 123 molecules

#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, ASP 182 TO ALA
Sequence detailsRNA: THE RNA MOLECULE USED FOR STRUCTURE DETERMINATION HAS THE FULL SEQUENCE. 5'- ...RNA: THE RNA MOLECULE USED FOR STRUCTURE DETERMINATION HAS THE FULL SEQUENCE. 5'-CCCCCCCCGAAAGGGGGGGGAAAAAAAAAAAAAAA

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8 / Details: 40% PEG 400 50 MM TRIS-HCL PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 34014 / % possible obs: 95.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.8 / % possible all: 66.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JE6

2je6


Resolution: 2.33→42.95 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.504 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1790 5 %RANDOM
Rwork0.205 ---
obs0.207 34014 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.67 Å2
Refinement stepCycle: LAST / Resolution: 2.33→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 112 16 122 5554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225621
X-RAY DIFFRACTIONr_bond_other_d0.0010.025323
X-RAY DIFFRACTIONr_angle_refined_deg1.4232.0137697
X-RAY DIFFRACTIONr_angle_other_deg0.792312367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0075741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7824.718195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84615907
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8691526
X-RAY DIFFRACTIONr_chiral_restr0.0760.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021008
X-RAY DIFFRACTIONr_nbd_refined0.2070.21142
X-RAY DIFFRACTIONr_nbd_other0.1810.25600
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22724
X-RAY DIFFRACTIONr_nbtor_other0.0860.23691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.2135
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5491.53689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90925815
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34432198
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.254.51867
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.39 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 129
Rwork0.261 2442

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