364D

3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA

• PDB DOI: https://doi.org/10.2210/pdb364D/pdb
• Entry: 364D supersedes: 356D
• NAKB: 364D

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


• Deposited: 1997-12-08 Released: 1998-01-02 
• 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: 3.00 Å
• R-Value Free: 0.324 
• R-Value Work: 0.272 
• R-Value Observed: 0.272 

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 of 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.

Macromolecule Content

• Total Structure Weight: 20 kDa 
• Atom Count: 1,311 
• Modelled Residue Count: 61 
• Deposited Residue Count: 61 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*UP*GP*GP*CP*GP*GP*C)-3')	A	11	Escherichia coli

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G *UP*C)-3')	B	19	Escherichia coli

Entity ID: 3
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP*GP*CP*CP*AP*GP*GP*CP*AP*U)-3')	C	31	Escherichia coli

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.324 
• R-Value Work: 0.272 
• R-Value Observed: 0.272 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.03	α = 90
b = 59.03	β = 90
c = 254.07	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-02 
Deposition Author(s): Correll, C.C., Freeborn, B., Moore, P.B., Steitz, T.A.
• This entry supersedes: 356D

Revision History  

• Version 1.0: 1998-01-02
  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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations