Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.24 kDa 
• Atom Count: 1004 
• Modelled Residue Count: 43 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

2FQN

Crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site

• PDB DOI: 10.2210/pdb2FQN/pdb
• NDB: AR0066

• Classification: RNA
• Mutation(s): No 


• Deposited: 2006-01-18 Released: 2006-02-14 
• Deposition Author(s): Kondo, J., Urzhumtsev, A., Westhof, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.247 

Literature

Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.

Kondo, J., Urzhumtsev, A., Westhof, E.

(2006) Nucleic Acids Res 34: 676-685

• PubMed: 16452297 
• DOI: 10.1093/nar/gkj467
• Primary Citation of Related Structures:  
  2FQN


• PubMed Abstract: 
  

The decoding A site of the small ribosomal subunit is an RNA molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. We have solved the crystal structure of an RNA fragment containing two Homo sapiens cytoplasmic A sites. Each of the two A sites presents a different conformational state. In one state, adenines A1492 and A1493 are fully bulged-out with C1409 forming a wobble-like pair to A1491. In the second state, adenines A1492 and A1493 form non-Watson-Crick pairs with C1409 and G1408, respectively while A1491 bulges out. The first state of the eukaryotic A site is, thus, basically the same as in the bacterial A site with bulging A1492 and A1493. It is the state used for recognition of the codon/anticodon complex. On the contrary, the second state of the H.sapiens cytoplasmic A site is drastically different from any of those observed for the bacterial A site without bulging A1492 and A1493.

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Organizational Affiliation: 

Institut de Biologie Moléculaire et Cellulaire, UPR9002 CNRS, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'	A, B	23	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	D [auth A], E [auth A], G [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-FGTKAUEHAT
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.247 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.05	α = 90
b = 47.39	β = 90
c = 56.76	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-01-18 
• Released Date: 2006-02-14 
Deposition Author(s): Kondo, J., Urzhumtsev, A., Westhof, E.

Revision History  

• Version 1.0: 2006-02-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance