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- PDB-3m85: Archaeoglobus fulgidus exosome y70a with RNA bound to the active site -

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Basic information

Entry
Database: PDB / ID: 3m85
TitleArchaeoglobus fulgidus exosome y70a with RNA bound to the active site
Components
  • (Probable exosome complex exonuclease ...) x 2
  • 5'-R(*CP*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


exosome (RNase complex) / RNA catabolic process / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / 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 / Exoribonuclease, phosphorolytic domain 2 ...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 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ubiquitin Ligase Nedd4; Chain: W; / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S5; domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 domain / Single Sheet / 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
RNA / Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Csl4
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
archaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 17, 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(*CP*UP*CP*CP*CP*C)-3'
Y: 5'-R(*CP*UP*CP*CP*CP*C)-3'
Z: 5'-R(*CP*UP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,77215
Polymers236,57512
Non-polymers1963
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31610 Å2
ΔGint-140 kcal/mol
Surface area81290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.020, 138.020, 262.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11F-263-

HOH

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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: 28585.512 Da / Num. of mol.: 3 / Mutation: Y70A
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(*CP*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, 9 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 / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M 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: SLS / Beamline: X06SA / Wavelength: 1.006 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2006
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 51207 / Num. obs: 51203 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.1 Å / Redundancy: 7.22 % / Num. unique all: 50904 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.4_129)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AB1

2ab1


Resolution: 3→19.984 Å / SU ML: 0.38 / σ(F): 1.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 5167 10.09 %random
Rwork0.1906 ---
all0.2 51207 --
obs0.1995 50904 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.417 Å2 / ksol: 0.28 e/Å3
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 3→19.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15861 240 3 6 16110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916330
X-RAY DIFFRACTIONf_angle_d1.25622047
X-RAY DIFFRACTIONf_dihedral_angle_d25.43910421
X-RAY DIFFRACTIONf_chiral_restr0.0792532
X-RAY DIFFRACTIONf_plane_restr0.0052861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.03440.32311480.22561437X-RAY DIFFRACTION97
3.0344-3.070.33871700.22981526X-RAY DIFFRACTION100
3.07-3.10730.30681600.22141502X-RAY DIFFRACTION100
3.1073-3.14640.35241660.21281549X-RAY DIFFRACTION100
3.1464-3.18770.31111600.21561495X-RAY DIFFRACTION100
3.1877-3.23120.30641850.20631495X-RAY DIFFRACTION100
3.2312-3.27710.31931910.20591485X-RAY DIFFRACTION100
3.2771-3.32580.30551730.19881513X-RAY DIFFRACTION100
3.3258-3.37760.2871890.20231517X-RAY DIFFRACTION100
3.3776-3.43270.27231730.17621523X-RAY DIFFRACTION100
3.4327-3.49160.27391740.19331499X-RAY DIFFRACTION100
3.4916-3.55470.30351700.18571531X-RAY DIFFRACTION100
3.5547-3.62270.25911810.18591501X-RAY DIFFRACTION100
3.6227-3.69620.29611820.18421496X-RAY DIFFRACTION100
3.6962-3.7760.29051590.19051537X-RAY DIFFRACTION100
3.776-3.86320.2821740.18621530X-RAY DIFFRACTION100
3.8632-3.95910.25821750.15871521X-RAY DIFFRACTION100
3.9591-4.06530.24311860.15121525X-RAY DIFFRACTION100
4.0653-4.18390.24941720.15231534X-RAY DIFFRACTION100
4.1839-4.31760.2451840.15581520X-RAY DIFFRACTION100
4.3176-4.47030.27651520.15111554X-RAY DIFFRACTION100
4.4703-4.64710.20111570.14431554X-RAY DIFFRACTION100
4.6471-4.85570.23881690.14241545X-RAY DIFFRACTION100
4.8557-5.10770.25021420.15721582X-RAY DIFFRACTION100
5.1077-5.42170.28131910.17781532X-RAY DIFFRACTION100
5.4217-5.83060.29441840.19611558X-RAY DIFFRACTION100
5.8306-6.39980.29561750.20961558X-RAY DIFFRACTION100
6.3998-7.28630.29751610.22071621X-RAY DIFFRACTION100
7.2863-9.03650.24261640.1931621X-RAY DIFFRACTION100
9.0365-19.98480.25712000.21861675X-RAY DIFFRACTION100

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