Yeast tRNAPhe: A Tour of the Structure Introduction: This Chime-based tutorial displays the secondary and tertiary structural features of yeast tRNAPhe. It is designed to complement the description in Saenger, W. (1984) Principles of Nucleic Acid Structure Ch. 15 "tRNA-A Treasury of Stereochemical Information". It is also based on the figures and descriptions in:
Sussman, J.L. et al. (1978) "Crystal Structure of Yeast Phenylalanine Transfer RNA I. Crystallographic Refinement" J. Mol. Biol.123 607.
Holbrook, S.R. et al. (1978) "II. Structural Features and Functional Implications." J. Mol. Biol.123 631.

Most of the tRNA Tour uses the "tRNA.pdb" coordinate file. This is the PDB-deposited "6TNA" file without H2O and without Mg2+. In addition, the average B-factors for phosphate groups (from Sussman, et al. ) were added to each of the P ATOM lines for display in Selection 3.
The close up views of teriary interactions in Selection 4 used RasMol-generated pdb files that include one residue on either side of the highlighted nucleotides.

PDB Abbreviations for Modified Nucleosides in tRNAPhe
Full Name of NucleosideStandard
16 & 17H2UDihydrouridineD or hU
26M2GN2, N2-DimethylguanosineM22G
39 & 55PSUPseudouridineY   "Psi"
40 & 495MC5-MethylcytidineM5C

These three-letter abbreviations appear on the images when the indicated residues are labeled. All other residues are identified as the standard A, C, G, or U nucleotides.
  *From the header (remark 5) of 6tna.pdb: "The modified base (Y-base) in this tRNA is commonly called 'wybutosine'. The systematic name for the base part of this nucleotide is 1H-Imidazo(1,2-alpha)purine-7-5 butanoic acid,4,9-dihydro-alpha-((methoxycarbonyl)amino)-5 4,6-dimethyl-9-oxo-methyl Ester. In reality the preceeding is a highly modified guanosine. It is linked to the ribose via the standard N9-C1' bond."!
A compilation of many other RNA modifications can be found at The RNA Modification Database.

Please note: The images displayed in this tutorial require the Chemscape Chime plug-in. In addition to simply displaying the molecular structures on a WWW page, the Chime plug-in allows the viewer to manipulate the image with pull-down menu choices, mouse and keyboard actions, and button-clicks. A demonstration of these additional features can be found at the Chime Features page.

Go to the tRNA Structure Tutorial

[This tutorial is also available as a "RasMol animation", i.e. a set of linked scripts that can be run on a computer using the RasMol v2.6 program. A description of the animation and downloading instructions are on the RasMol Animation page.]

Back to Molecular Models for Biochemistry at CMU.

Dr. William McClure
Department of Biological Sciences
Carnegie Mellon University
Pittsburgh, PA 15213