Biological Assembly 1  

 3D View: Structure

Pseudo Symmetry: Cyclic - C3  (3D View)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 9-mer - A3BC 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 249.47 kDa 
• Atom Count: 16910 
• Residue Count: 2154 
• Unique protein chains: 3

2BA0

Archaeal exosome core

• DOI: 10.2210/pdb2BA0/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-13 Released: 2005-11-22 
• Deposition Author(s): Buttner, K., Wenig, K., Hopfner, K.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 

Literature

Structural framework for the mechanism of archaeal exosomes in RNA processing.

Buttner, K., Wenig, K., Hopfner, K.P.

(2005) Mol Cell 20: 461-471

• PubMed: 16285927 
• DOI: 10.1016/j.molcel.2005.10.018
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Exosomes emerge as central 3'-->5' RNA processing and degradation machineries in eukaryotes and archaea. We determined crystal structures of two 230 kDa nine subunit archaeal exosome isoforms. Both exosome isoforms contain a hexameric ring of RNase phosphorolytic (PH) domain subunits with a central chamber. Tungstate soaks identified three phosphorolytic active sites in this processing chamber. A trimer of Csl4 or Rrp4 subunits forms a multidomain macromolecular interaction surface on the RNase-PH domain ring with central S1 domains and peripheral KH and zinc-ribbon domains. Structural and mutational analyses suggest that the S1 domains and a subsequent neck in the RNase-PH domain ring form an RNA entry pore to the processing chamber that only allows access of unstructured RNA. This structural framework can mechanistically unify observed features of exosomes, including processive degradation of unstructured RNA, the requirement for regulatory factors to degrade structured RNA, and left-over tails in rRNA trimming.

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Organizational Affiliation: 

Gene Center and Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Archaeal exosome RNA binding protein RRP4	A, B, C	229	Archaeoglobus fulgidus	Mutation(s): 0
Find proteins for O29758 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Explore O29758  Go to UniProtKB:  O29758

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Archaeal exosome RNA binding protein RRP41	D, E, F	258	Archaeoglobus fulgidus	Mutation(s): 0  EC: 3.1.13
Find proteins for O29757 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Explore O29757  Go to UniProtKB:  O29757

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Archaeal exosome RNA binding protein RRP42	G, H, I	259	Archaeoglobus fulgidus	Mutation(s): 0  EC: 3.1.13
Find proteins for O29756 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)) Explore O29756  Go to UniProtKB:  O29756

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.264 
• R-Value Work: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.57	α = 90
b = 129.59	β = 101.56
c = 102.33	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
XDS	data reduction
SHELXS	phasing
CNS	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-13 
• Released Date: 2005-11-22 
Deposition Author(s): Buttner, K., Wenig, K., Hopfner, K.P.

Revision History 

• Version 1.0: 2005-11-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description