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- PDB-3m7n: archaeoglobus fulgidus exosome with RNA bound to the active site -

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Basic information

Entry
Database: PDB / ID: 3m7n
Titlearchaeoglobus fulgidus exosome with RNA bound to the active site
Components
  • (Probable exosome complex exonuclease ...) x 2
  • 5'-R(*C*UP*CP*CP*CP*C)-3'
  • Putative uncharacterized protein AF_0206
KeywordsHYDROLASE/RNA / exosome / RNA / Exonuclease / Hydrolase / Nuclease / HYDROLASE-RNA complex
Function / homology
Function and homology information


cytoplasmic exosome (RNase complex) / exosome (RNase complex) / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / gene expression / RNA binding ...cytoplasmic exosome (RNase complex) / exosome (RNase complex) / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / gene expression / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Exosome complex component Csl4, archaea / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 / GHMP Kinase, N-terminal domain / : ...Exosome complex component Csl4, archaea / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / 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 / GHMP Kinase, N-terminal domain / : / : / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S5; domain 2 / Single Sheet / 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 / Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Csl4
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHartung, S. / Hopfner, K.-P.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Quantitative analysis of processive RNA degradation by the archaeal RNA exosome
Authors: Hartung, S. / Niederberger, T. / Hartung, M. / Tresch, A. / Hopfner, K.-P.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein AF_0206
B: Putative uncharacterized protein AF_0206
C: Putative uncharacterized protein AF_0206
D: Probable exosome complex exonuclease 1
E: Probable exosome complex exonuclease 1
F: Probable exosome complex exonuclease 1
G: Probable exosome complex exonuclease 2
H: Probable exosome complex exonuclease 2
I: Probable exosome complex exonuclease 2
X: 5'-R(*C*UP*CP*CP*CP*C)-3'
Y: 5'-R(*C*UP*CP*CP*CP*C)-3'
Z: 5'-R(*C*UP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,04815
Polymers236,85212
Non-polymers1963
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31580 Å2
ΔGint-147 kcal/mol
Surface area81720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.268, 138.268, 262.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Probable exosome complex exonuclease ... , 2 types, 6 molecules DEFGHI

#2: Protein Probable exosome complex exonuclease 1 / exosome RNA binding protein Rrp41


Mass: 28860.266 Da / Num. of mol.: 3 / Mutation: R65E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0493 / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: O29757, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein Probable exosome complex exonuclease 2 / exosome RNA binding protein Rrp42


Mass: 28677.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0494 / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: O29756, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Protein / RNA chain , 2 types, 6 molecules ABCXYZ

#1: Protein Putative uncharacterized protein AF_0206 / exosome RNA binding protein Csl4


Mass: 19625.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0206 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O30033
#4: RNA chain 5'-R(*C*UP*CP*CP*CP*C)-3'


Mass: 1787.117 Da / Num. of mol.: 3 / Source method: obtained synthetically

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Non-polymers , 2 types, 719 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Na Acetate, pH 4.6, 30% MPD, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 94454 / Num. obs: 94417 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 42.22 Å2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 86.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_129)refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BA1

2ba1


Resolution: 2.4→48.057 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.83 / SU ML: 0.41 / σ(F): 1.96 / σ(I): 2 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 5026 5.05 %RANDOM
Rwork0.1971 94428 --
all0.27 99465 --
obs0.2 89224 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.018 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 153.88 Å2 / Biso mean: 49.712 Å2 / Biso min: 17.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.483 Å20 Å2-0 Å2
2--2.483 Å20 Å2
3----4.966 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15866 274 3 716 16859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816376
X-RAY DIFFRACTIONf_angle_d1.12922120
X-RAY DIFFRACTIONf_dihedral_angle_d18.8646361
X-RAY DIFFRACTIONf_chiral_restr0.0692541
X-RAY DIFFRACTIONf_plane_restr0.0042862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.42750.27471620.22962976X-RAY DIFFRACTION95
2.4275-2.45610.28551880.22453054X-RAY DIFFRACTION100
2.4561-2.4860.28081700.21413071X-RAY DIFFRACTION100
2.486-2.51750.29091810.21673139X-RAY DIFFRACTION100
2.5175-2.55060.31271610.2173107X-RAY DIFFRACTION100
2.5506-2.58550.28731650.21323095X-RAY DIFFRACTION100
2.5855-2.62250.27741670.20823129X-RAY DIFFRACTION100
2.6225-2.66160.27391650.20563128X-RAY DIFFRACTION100
2.6616-2.70320.28891610.20573106X-RAY DIFFRACTION100
2.7032-2.74750.30991660.2143100X-RAY DIFFRACTION100
2.7475-2.79490.3231600.22143153X-RAY DIFFRACTION100
2.7949-2.84570.32171620.22293113X-RAY DIFFRACTION100
2.8457-2.90040.29191720.21813114X-RAY DIFFRACTION100
2.9004-2.95960.28481670.21123148X-RAY DIFFRACTION100
2.9596-3.0240.29341970.2093093X-RAY DIFFRACTION100
3.024-3.09430.28871870.20683111X-RAY DIFFRACTION100
3.0943-3.17170.26331680.19543116X-RAY DIFFRACTION100
3.1717-3.25740.26651650.18773157X-RAY DIFFRACTION100
3.2574-3.35320.26011410.19863158X-RAY DIFFRACTION100
3.3532-3.46140.25831590.19093176X-RAY DIFFRACTION100
3.4614-3.58510.22211750.18533133X-RAY DIFFRACTION100
3.5851-3.72860.22641550.17473158X-RAY DIFFRACTION100
3.7286-3.89820.23351560.17123189X-RAY DIFFRACTION100
3.8982-4.10360.2221630.17373162X-RAY DIFFRACTION100
4.1036-4.36060.191550.15493206X-RAY DIFFRACTION100
4.3606-4.6970.21071780.1533185X-RAY DIFFRACTION100
4.697-5.16920.19311900.16283195X-RAY DIFFRACTION100
5.1692-5.9160.26171750.1843231X-RAY DIFFRACTION100
5.916-7.44910.27641560.20093292X-RAY DIFFRACTION100
7.4491-48.06710.21781590.20443433X-RAY DIFFRACTION98

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