Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61440.45 
• Atom Count: 3539 
• Residue Count: 399 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2FK6

Crystal Structure of RNAse Z/tRNA(Thr) complex

• DOI: 10.2210/pdb2FK6/pdb
• NDB: PR0190

• Classification: HYDROLASE/RNA
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli
• Mutation(s): 3 


• Deposited: 2006-01-04 Released: 2006-03-21 
• Deposition Author(s): Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O., Condon, C.

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Experimental Data Snapshot

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

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

• PubMed: 16518398 
• 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 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.

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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




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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
Molecule	Chains	Sequence Length	Organism	Details
RIBONUCLEASE Z	A	320	Bacillus subtilis (strain 168)	Mutation(s): 3  Gene Names: rnz (yqjK) EC: 3.1.26.11
Find proteins for P54548 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P54548

Entity ID: 1
Molecule	Chains	Length	Organism
TRNA(THR)	R	79	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MES	A	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

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 = 173.540	α = 90.00
b = 42.400	β = 121.42
c = 110.430	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-04 
• Released Date: 2006-03-21 
• Deposition Author(s): Li de la Sierra-Gallay, I., Mathy, N., Pellegrini, O., Condon, C.

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