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Molecular Biology · Nucleic acid

Transfer RNA 3D Structure

The adaptor of protein synthesis: an L-shaped RNA of 76 nucleotides that reads a codon at one end and carries an amino acid at the other.

A transfer RNA links the genetic code to amino acids. Its anticodon pairs with a codon of messenger RNA in the ribosome, and its other end carries the amino acid that codon stands for. Drawn flat, its four stems make a cloverleaf; in three dimensions they fold into an L. This is the tRNA for phenylalanine from baker's yeast, the first tRNA whose structure was solved, in 1974.

Also called tRNA or tRNA for phenylalanine.

Transfer RNA as a grey ribbon folded into an L shape, with its bases as rungs: the anticodon loop at the end of one arm and the CCA end at the end of the other.
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An RNA folded into an L

The tRNA's single chain of 76 nucleotides pairs with itself into four short stems, then folds so that pairs of stems stack into two arms at right angles. The anticodon and the amino acid end up about 7 nanometres apart, at the two ends of the L.

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View 1 of 6: An RNA folded into an L

Download the pictureDownload the atoms (PDB)Checked against its sources on 25 October 2026.

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The Transfer RNA structure, explained

  1. 01An RNA folded into an L

    The tRNA's single chain of 76 nucleotides pairs with itself into four short stems, then folds so that pairs of stems stack into two arms at right angles. The anticodon and the amino acid end up about 7 nanometres apart, at the two ends of the L.

  2. 02Where the amino acid goes

    The acceptor stem ends in four unpaired nucleotides, the last three always CCA. An enzyme matched to this tRNA, phenylalanyl-tRNA synthetase, joins phenylalanine to the final A, so the tRNA is charged.

  3. 03Where the code is read

    At the other end of the L, the anticodon loop holds three unpaired bases, here Gm, A and A. In the ribosome they pair with a codon of the messenger RNA, UUC or UUU, both codons for phenylalanine.

  4. 04Four arms of a cloverleaf

    Drawn flat, the tRNA is a cloverleaf of four stems: the acceptor stem, the D arm, the anticodon arm and the TΨC arm. In three dimensions the acceptor stem stacks on the TΨC arm, and the D arm on the anticodon arm.

  5. 05Held at the corner

    The loops of the D and TΨC arms meet at the corner of the L, where bases from each pair and stack with each other. These tertiary contacts, with magnesium ions, hold the two arms at right angles.

  6. 06Fourteen modified nucleotides

    Enzymes change many of a tRNA's bases after it is made. In this one, wybutosine sits just beside the anticodon, where it steadies codon pairing, and the modifications of the D and TΨC loops help fold the corner.

Parts

What each part does

Acceptor stem
The first seven nucleotides paired with seven near the far end: a short double helix that ends in the single-stranded tail where the amino acid is attached.
CCA end
The last three nucleotides, always C, C, A. The amino acid is joined to the sugar of the final A by an aminoacyl-tRNA synthetase.
D arm
A stem and loop named for the dihydrouridines in its loop. It folds against the T arm at the corner of the L.
Anticodon arm
A stem and a loop of seven nucleotides at the bottom of the L, which reaches into the ribosome to pair with messenger RNA.
Anticodon
Gm, A, A (5′ to 3′): three bases that pair with the codons UUC and UUU for phenylalanine, the second through a wobble pair at the third position.
Variable loop
A short loop between the anticodon arm and the T arm. Its length differs most from one tRNA to another.
TΨC arm
A stem and loop named for thymine, pseudouridine and cytosine in its loop. It stacks on the acceptor stem to make one long arm of the L.
Modified nucleotides
Fourteen of the 76 nucleotides are chemically changed after the RNA is made: methylated bases and sugars, dihydrouridine, pseudouridine and wybutosine beside the anticodon. They help the tRNA fold and read codons accurately.
Magnesium ions
Positive ions bound where the folded RNA brings its negative phosphates close together. They help hold the L shape.

The structure

Where these atoms come from

Structure
PDB 1EHZ
What it is
Yeast tRNA for phenylalanine
Organism
Saccharomyces cerevisiae
Method
X-ray diffraction, 1.93 Å resolution
Deposited
2000
Atoms shown
1,658, without water or hydrogens
Paper
Shi H and others, RNA 2000

Coordinates from the Protein Data Bank, free of all copyright (CC0). Water and hydrogens are left out, and the molecule is turned to face you; every atom is where the experiment placed it.

Dictionary

The terms to know

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The quizzes and cards that fit

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Sources

Where the facts come from

Written by biofideX from these sources. Drawn with 3Dmol.js (Rego and Koes, Bioinformatics 2015).

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