4M30

Crystal structure of RNASE III complexed with double-stranded RNA AND AMP (TYPE II CLEAVAGE)

• PDB DOI: https://doi.org/10.2210/pdb4M30/pdb
• NAKB: 4M30

• Classification: HYDROLASE/RNA
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2013-12-11 
• Deposition Author(s): Gan, J., Liang, Y.-H., Shaw, G.X., Tropea, J.E., Waugh, D.S., Ji, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

RNase III: Genetics and Function; Structure and Mechanism.

Court, D.L., Gan, J., Liang, Y.H., Shaw, G.X., Tropea, J.E., Costantino, N., Waugh, D.S., Ji, X.

(2013) Annu Rev Genet 47: 405-431

• PubMed: 24274754 
• DOI: https://doi.org/10.1146/annurev-genet-110711-155618
• Primary Citation of Related Structures:  
  4M2Z, 4M30


• PubMed Abstract: 
  

  RNase III is a global regulator of gene expression in Escherichia coli that is instrumental in the maturation of ribosomal and other structural RNAs. We examine here how RNase III itself is regulated in response to growth and other environmental changes encountered by the cell and how, by binding or processing double-stranded RNA (dsRNA) intermediates, RNase III controls the expression of genes. Recent insight into the mechanism of dsRNA binding and processing, gained from structural studies of RNase III, is reviewed. Structural studies also reveal new cleavage sites in the enzyme that can generate longer 3' overhangs.

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Organizational Affiliation: 

Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702; email: [e-mail] , [e-mail] , [e-mail] , [e-mail] , [e-mail] , [e-mail] , [e-mail] , [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 70.63 kDa 
• Atom Count: 4,944 
• Modelled Residue Count: 492 
• Deposited Residue Count: 496 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease 3	A, B	221	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: aq_946, rnc EC: 3.1.26.3
UniProt
Find proteins for O67082 (Aquifex aeolicus (strain VF5)) Explore O67082  Go to UniProtKB:  O67082

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA12	C, D	27	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A	L [auth C], P [auth D]	ADENOSINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MPD	I [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG	E [auth A], F [auth A], G [auth B], H [auth B], J [auth C], K [auth C], M [auth D], N [auth D], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.104	α = 90
b = 81.104	β = 90
c = 223.962	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Gan, J., Liang, Y.-H., Shaw, G.X., Tropea, J.E., Waugh, D.S., Ji, X.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-20
  Changes: Refinement description