354D | pdb_0000354d

Structure of loop E FROM E. coli 5S RRNA

• PDB DOI: https://doi.org/10.2210/pdb354D/pdb
• NAKB: 354D

• Classification: RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-10-01 Released: 1997-11-26 
• Deposition Author(s): Correll, C.C., Freeborn, B., Moore, P.B., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.228 (Depositor) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.

Correll, C.C., Freeborn, B., Moore, P.B., Steitz, T.A.

(1997) Cell 91: 705-712

• PubMed: 9393863 
• DOI: https://doi.org/10.1016/s0092-8674(00)80457-2
• Primary Citation Related Structures: 
  354D, 357D, 364D


• PubMed Abstract: 
  

  Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, Connecticut 06520-8114, USA.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.92 kDa 
• Atom Count: 647 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*G)-3')	A	12	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA-DNA (5'-R(*GP*CP*GP*AP*GP*AP*GP*UP*AP*)-D(*DGP(S)*)-R(*GP*C)-3')	B	12	Escherichia coli

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.228 (Depositor) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.184	α = 90
b = 37.654	β = 105.9
c = 32.944	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
CNS	refinement
DENZO	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-26 
Deposition Author(s): Correll, C.C., Freeborn, B., Moore, P.B., Steitz, T.A.

Revision History  

• Version 1.0: 1997-11-26
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2015-02-18
  Changes: Non-polymer description
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Derived calculations