3L0U

The crystal structure of unmodified tRNAPhe from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb3L0U/pdb
• NAKB: 3L0U

• Classification: RNA
• Organism(s): Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2009-12-10 Released: 2010-03-16 
• Deposition Author(s): Byrne, R.T., Konevega, A.L., Rodnina, M.V., Antson, A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

The crystal structure of unmodified tRNAPhe from Escherichia coli

Byrne, R.T., Konevega, A.L., Rodnina, M.V., Antson, A.A.

(2010) Nucleic Acids Res 38: 4154-4162

• PubMed: 20203084 
• DOI: https://doi.org/10.1093/nar/gkq133
• Primary Citation of Related Structures:  
  3L0U


• PubMed Abstract: 
  

  Post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer RNA (tRNA) so that it is optimized for participation in cellular processes. Here we report the crystal structure of unmodified tRNA(Phe) from Escherichia coli at a resolution of 3 A. We show that in the absence of modifications the overall fold of the tRNA is essentially the same as that of mature tRNA. However, there are a number of significant structural differences, such as rearrangements in a triplet base pair and a widened angle between the acceptor and anticodon stems. Contrary to previous observations, the anticodon adopts the same conformation as seen in mature tRNA.

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Organizational Affiliation: 

York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, North Yorkshire, YO10 5YW, UK.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 24.57 kDa 
• Atom Count: 1,573 
• Modelled Residue Count: 73 
• Deposited Residue Count: 76 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Unmodified tRNAPhe	A	76	Escherichia coli K-12

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.45	α = 90
b = 99.45	β = 90
c = 110.33	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-16 
Deposition Author(s): Byrne, R.T., Konevega, A.L., Rodnina, M.V., Antson, A.A.

Revision History  

• Version 1.0: 2010-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2019-12-25
  Changes: Advisory, Data collection, Source and taxonomy
• Version 1.4: 2021-11-10
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-11-01
  Changes: Data collection, Refinement description