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- PDB-2ba1: Archaeal exosome core -

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Basic information

Entry
Database: PDB / ID: 2ba1
TitleArchaeal exosome core
Components
  • Archaeal exosome RNA binding protein CSL4
  • Archaeal exosome complex exonuclease RRP41
  • Archaeal exosome complex exonuclease RRP42
KeywordsRNA BINDING PROTEIN / EXOSOME / RNASE PH / RNA DEGRADATION / EXORIBONUCLEASE / RNA BINDING / S1 DOMAIN / ZN-RIBBON / ARCHAEAL / PHOSPHOROLYTIC
Function / homology
Function and homology information


exosome (RNase complex) / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 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) / : ...exosome (RNase complex) / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 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 / 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 / Ubiquitin Ligase Nedd4; Chain: W; - #10 ...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 / 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 / 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
Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Csl4
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsHopfner, K.P. / Buttner, K. / Wenig, K.
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 ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 CSL4
C: Archaeal exosome RNA binding protein CSL4
B: Archaeal exosome RNA binding protein CSL4
E: Archaeal exosome complex exonuclease RRP41
D: Archaeal exosome complex exonuclease RRP41
F: Archaeal exosome complex exonuclease RRP41
H: Archaeal exosome complex exonuclease RRP42
G: Archaeal exosome complex exonuclease RRP42
I: Archaeal exosome complex exonuclease RRP42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,77112
Polymers231,5759
Non-polymers1963
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26860 Å2
ΔGint-93 kcal/mol
Surface area82150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.460, 137.460, 261.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Archaeal 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) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O30033
#2: Protein Archaeal exosome complex exonuclease 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 complex exonuclease 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Sodium acetate, 32% MPD, 10mM NaCl, pH 5.6, 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)
SYNCHROTRONSLS X06SA11.01
SYNCHROTRONESRF ID2920.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 1, 2005
ADSC QUANTUM 42CCDMay 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.011
20.9791
ReflectionResolution: 2.7→20 Å / Num. all: 69124 / Num. obs: 69124 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.08
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.9

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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
Rfree0.275 1929 RANDOM
Rwork0.224 --
all-69041 -
obs-69041 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15660 0 3 83 15746
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007

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