3L7Z

Crystal structure of the S. solfataricus archaeal exosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring.

Lu, C.Ding, F.Ke, A.

(2010) PLoS One 5: e8739-e8739

  • DOI: 10.1371/journal.pone.0008739
  • Primary Citation of Related Structures:  
    3L7Z

  • PubMed Abstract: 
  • The exosome complex is an essential RNA 3'-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable exosome complex exonuclease 2A, D, G271Saccharolobus solfataricusMutation(s): 1 
Gene Names: C20_023Rrp41/42/4SSO0732
EC: 3.1.13
UniProt
Find proteins for Q9UXC0 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC0 
Go to UniProtKB:  Q9UXC0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXC0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Probable exosome complex exonuclease 1B, E, H245Saccharolobus solfataricusMutation(s): 0 
Gene Names: SSO0735
EC: 3.1.13
UniProt
Find proteins for Q9UXC2 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC2 
Go to UniProtKB:  Q9UXC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXC2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable exosome complex RNA-binding protein 1C, F, I249Saccharolobus solfataricusMutation(s): 0 
Gene Names: C20_026SSO0736
UniProt
Find proteins for Q9UXC4 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q9UXC4 
Go to UniProtKB:  Q9UXC4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UXC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth B],
K [auth E],
L [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.266 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.122α = 90
b = 145.484β = 93.79
c = 97.245γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations