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- PDB-2jeb: Structure of a 9-subunit archaeal exosome bound to Mn ions -

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Basic information

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


cytoplasmic exosome (RNase complex) / CUT catabolic process / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / 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) / : / rRNA catabolic process / poly(A) binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters ...cytoplasmic exosome (RNase complex) / CUT catabolic process / U4 snRNA 3'-end processing / poly(A)-dependent snoRNA 3'-end processing / 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) / : / rRNA catabolic process / poly(A) binding / 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 / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / GHMP Kinase, N-terminal domain / K Homology domain, type 1 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 ...Exosome complex component Rrp4 / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / : / Exosome complex RNA-binding protein 1/RRP40/RRP4 / KH domain / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 domain / Nucleic acid-binding proteins / 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
: / 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: 2.4 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_conn / 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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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,

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,7967
Polymers86,4123
Non-polymers3844
Water3,027168
1
A: EXOSOME COMPLEX EXONUCLEASE 2
B: EXOSOME COMPLEX EXONUCLEASE 1
I: EXOSOME COMPLEX RNA-BINDING PROTEIN 1
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)260,38821
Polymers259,2379
Non-polymers1,15112
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
MethodPQS
Unit cell
Length a, b, c (Å)133.640, 133.640, 133.640
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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Protein , 1 types, 1 molecules I

#3: Protein EXOSOME COMPLEX RNA-BINDING PROTEIN 1


Mass: 28225.387 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 , 4 types, 172 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, ASP 182 TO ALA

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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: 1.55
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 29796 / % possible obs: 99.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 97.6

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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: 2.4→44.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.313 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.397 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1568 5 %RANDOM
Rwork0.198 ---
obs0.201 29796 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: 45.36 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 19 168 5426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225348
X-RAY DIFFRACTIONr_bond_other_d0.0010.025129
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9897277
X-RAY DIFFRACTIONr_angle_other_deg0.745311892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3724.794194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.91415883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2561526
X-RAY DIFFRACTIONr_chiral_restr0.070.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
X-RAY DIFFRACTIONr_nbd_refined0.1880.21109
X-RAY DIFFRACTIONr_nbd_other0.180.25508
X-RAY DIFFRACTIONr_nbtor_refined0.170.22616
X-RAY DIFFRACTIONr_nbtor_other0.0860.23495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.2169
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4611.53735
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69925635
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.05631983
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6214.51640
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: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 116
Rwork0.23 2197

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