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- PDB-2ba0: Archaeal exosome core -

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Basic information

Entry
Database: PDB / ID: 2ba0
TitleArchaeal exosome core
Components
  • Archaeal exosome RNA binding protein RRP4
  • Archaeal exosome RNA binding protein RRP41
  • Archaeal exosome RNA binding protein RRP42
KeywordsRNA BINDING PROTEIN / EXOSOME / RNASE PH / RNA DEGRADATION / EXORIBONUCLEASE / RNA BINDING / S1DOMAIN / KH DOMAIN / ARCHAEAL
Function / homology
Function and homology information


exosome (RNase complex) / poly(A) binding / RNA catabolic process / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / 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 / Exoribonuclease, phosphorolytic domain 1 ...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 / KH domain / RNA-binding domain, S1 / K Homology domain, type 1 / Type-1 KH domain profile. / 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 RNA binding domain / S1 domain / Nucleic acid-binding proteins / K Homology domain / K homology RNA-binding 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
Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Rrp4
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsButtner, K. / Wenig, K. / Hopfner, K.P.
CitationJournal: Mol.Cell / Year: 2005
Title: Structural framework for the mechanism of archaeal exosomes in RNA processing.
Authors: Buttner, K. / Wenig, K. / Hopfner, K.P.
History
DepositionOct 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaeal exosome RNA binding protein RRP4
B: Archaeal exosome RNA binding protein RRP4
C: Archaeal exosome RNA binding protein RRP4
F: Archaeal exosome RNA binding protein RRP41
E: Archaeal exosome RNA binding protein RRP41
D: Archaeal exosome RNA binding protein RRP41
I: Archaeal exosome RNA binding protein RRP42
H: Archaeal exosome RNA binding protein RRP42
G: Archaeal exosome RNA binding protein RRP42


Theoretical massNumber of molelcules
Total (without water)249,4689
Polymers249,4689
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29110 Å2
ΔGint-84 kcal/mol
Surface area89380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.570, 129.590, 102.330
Angle α, β, γ (deg.)90.00, 101.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Archaeal exosome RNA binding protein RRP4


Mass: 25589.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O29758
#2: Protein Archaeal exosome RNA binding protein RRP41


Mass: 28888.348 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pET28 / 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 Archaeal 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) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: O29756, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M HEPES, 35% MPD, 10mM CaCl2, 15% Glycerol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.979
SYNCHROTRONESRF ID14-120.933
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 1, 2005
ADSC QUANTUM 42CCDMar 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9331
ReflectionResolution: 2.7→20 Å / Num. all: 69958 / Num. obs: 69958 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.1
Reflection shellResolution: 2.7→2.8 Å / % possible all: 84.4

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Processing

Software
NameVersionClassification
ProDCdata collection
XDSdata reduction
SHELXSphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.264 3589 RANDOM
Rwork0.216 --
all-69955 -
obs-69955 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16818 0 0 101 16919
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_bond_d0.008

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