2C37

RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural Basis of 3' End RNA Recognition and Exoribonucleolytic Cleavage by an Exosome Rnase Ph Core.

Lorentzen, E.Conti, E.

(2005) Mol Cell 20: 473

  • DOI: https://doi.org/10.1016/j.molcel.2005.10.020
  • Primary Citation of Related Structures:  
    2C37, 2C38, 2C39

  • PubMed Abstract: 

    The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
275Saccharolobus solfataricusMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
248Saccharolobus solfataricusMutation(s): 0 
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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U5P
Query on U5P

Download Ideal Coordinates CCD File 
AB [auth U]
BA [auth B]
BB [auth U]
CA [auth B]
CB [auth U]
AB [auth U],
BA [auth B],
BB [auth U],
CA [auth B],
CB [auth U],
EA [auth E],
EB [auth V],
FA [auth E],
GA [auth E],
GB [auth W],
HB [auth W],
IA [auth F],
IB [auth W],
JA [auth G],
KA [auth G],
KB [auth X],
MA [auth H],
NA [auth I],
OA [auth I],
QA [auth J],
SA [auth M],
TA [auth M],
VA [auth N],
Y [auth A],
Z [auth A]
URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
RP5
Query on RP5

Download Ideal Coordinates CCD File 
WA [auth N]5-O-phosphono-beta-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-TXICZTDVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
DA [auth D]
DB [auth V]
HA [auth F]
JB [auth X]
AA [auth B],
DA [auth D],
DB [auth V],
HA [auth F],
JB [auth X],
LA [auth H],
PA [auth J],
RA [auth L],
UA [auth N],
XA [auth P],
YA [auth R],
ZA [auth T]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
FB [auth V]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.267 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.02α = 90
b = 212.94β = 90
c = 433.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-23
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary