Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A4B2 

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

Macromolecule Content

• Total Structure Weight: 66.55 kDa 
• Atom Count: 4,754 
• Modelled Residue Count: 514 
• Deposited Residue Count: 515 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

 4OOG

Crystal structure of yeast RNase III (Rnt1p) complexed with the product of dsRNA processing

• PDB DOI: 10.2210/pdb4OOG/pdb
• NDB: NA2905

• Classification: HYDROLASE/RNA
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2014-02-02 Released: 2014-04-16 
• Deposition Author(s): Liang, Y.-H., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 

Literature

Structure of a Eukaryotic RNase III Postcleavage Complex Reveals a Double-Ruler Mechanism for Substrate Selection.

Liang, Y.H., Lavoie, M., Comeau, M.A., Abou Elela, S., Ji, X.

(2014) Mol Cell 54: 431-444

• PubMed: 24703949 
• DOI: 10.1016/j.molcel.2014.03.006
• Primary Citation of Related Structures:  
  4OOG


• PubMed Abstract: 
  

Ribonuclease III (RNase III) enzymes are a family of double-stranded RNA (dsRNA)-specific endoribonucleases required for RNA maturation and gene regulation. Prokaryotic RNase III enzymes have been well characterized, but how eukaryotic RNase IIIs work is less clear. Here, we describe the structure of the Saccharomyces cerevisiae RNase III (Rnt1p) postcleavage complex and explain why Rnt1p binds to RNA stems capped with an NGNN tetraloop. The structure shows specific interactions between a structural motif located at the end of the Rnt1p dsRNA-binding domain (dsRBD) and the guanine nucleotide in the second position of the loop. Strikingly, structural and biochemical analyses indicate that the dsRBD and N-terminal domains (NTDs) of Rnt1p function as two rulers that measure the distance between the tetraloop and the cleavage site. These findings provide a framework for understanding eukaryotic RNase IIIs.

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Organizational Affiliation: 

Biomolecular Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 3	A, B	110	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RNT1, YM9408.01C, YM9959.21, YMR239C EC: 3.1.26.3
UniProt
Find proteins for Q02555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02555  Go to UniProtKB:  Q02555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 3	C	261	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RNT1, YM9408.01C, YM9959.21, YMR239C EC: 3.1.26.3
UniProt
Find proteins for Q02555 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02555  Go to UniProtKB:  Q02555

Entity ID: 3
Molecule	Chains	Length	Organism	Image
34-mer RNA	D	34	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth C], F [auth C], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.239 
• R-Value Work: 0.216 
• R-Value Observed: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.972	α = 90
b = 183.804	β = 90
c = 61.289	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-16 
Deposition Author(s): Liang, Y.-H., Ji, X.

Revision History  

• Version 1.0: 2014-04-16
  Type: Initial release
  
• Version 1.1: 2014-05-28
  Changes: Database references