1DUH

CRYSTAL STRUCTURE OF THE CONSERVED DOMAIN IV OF E. COLI 4.5S RNA

• PDB DOI: https://doi.org/10.2210/pdb1DUH/pdb
• NAKB: 1DUH

• Classification: RNA
• Mutation(s): No 


• Deposited: 2000-01-17 Released: 2000-05-08 
• Deposition Author(s): Jovine, L., Hainzl, T., Oubridge, C., Scott, W.G., Li, J., Sixma, T.K., Wonacott, A., Skarzynski, T., Nagai, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.230 
• R-Value Observed: 0.244 

Literature

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.

Jovine, L., Hainzl, T., Oubridge, C., Scott, W.G., Li, J., Sixma, T.K., Wonacott, A., Skarzynski, T., Nagai, K.

(2000) Structure 8: 527-540

• PubMed: 10801497 
• DOI: https://doi.org/10.1016/s0969-2126(00)00137-4
• Primary Citation of Related Structures:  
  1DUH


• PubMed Abstract: 
  

  Bacterial signal recognition particle (SRP), consisting of 4.5S RNA and Ffh protein, plays an essential role in targeting signal-peptide-containing proteins to the secretory apparatus in the cell membrane. The 4.5S RNA increases the affinity of Ffh for signal peptides and is essential for the interaction between SRP and its receptor, protein FtsY. The 4.5S RNA also interacts with elongation factor G (EF-G) in the ribosome and this interaction is required for efficient translation.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, England. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.06 kDa 
• Atom Count: 988 
• Modelled Residue Count: 45 
• Deposited Residue Count: 45 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
4.5S RNA DOMAIN IV	A	45	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LU	B [auth A]	LUTETIUM (III) ION Lu PSDMOPINLDTFSZ-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.230 
• R-Value Observed: 0.244 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.697	α = 90
b = 69.697	β = 90
c = 84.102	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-08 
Deposition Author(s): Jovine, L., Hainzl, T., Oubridge, C., Scott, W.G., Li, J., Sixma, T.K., Wonacott, A., Skarzynski, T., Nagai, K.

Revision History  

• Version 1.0: 2000-05-08
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations