2FK6

Crystal Structure of RNAse Z/tRNA(Thr) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA.

Li de la Sierra-Gallay, I.Mathy, N.Pellegrini, O.Condon, C.

(2006) Nat.Struct.Mol.Biol. 13: 376-377

  • DOI: 10.1038/nsmb1066

  • PubMed Abstract: 
  • The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure ...

    The highly conserved ribonuclease RNase Z catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Here we present the structure of the complex between Bacillus subtilis RNase Z and tRNA(Thr), the first structure of a ribonucleolytic processing enzyme bound to tRNA. Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage.


    Related Citations: 
    • Structural basis for substrate binding, cleavage and allostery in the tRNA maturase RNase Z
      Li de la Sierra-Gallay, I.,Pellegrini, O.,Condon, C.
      (2005) Nature 433: 657


    Organizational Affiliation

    Centre National de la Recherche (CNRS) FRC550, Institut de Biologie Physico-Chimique, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE Z
A
320Bacillus subtilis (strain 168)Gene Names: rnz (yqjK)
EC: 3.1.26.11
Find proteins for P54548 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P54548
Entity ID: 1
MoleculeChainsLengthOrganism
TRNA(THR)R79N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 173.540α = 90.00
b = 42.400β = 121.42
c = 110.430γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description