The animation separates molecular structure from illustrated movement. No experimental trajectory is implied.
PDB 1I6H ↗RNA polymerase II
Yeast transcription complex, 3.3 Å. The protein shape is experimental when loaded; positioning against the teaching DNA is approximate.
PDB 9SPI ↗Human 80S ribosome
Cryo-EM structure, 2.4 Å, with A-, P- and E-site tRNAs. The original complex can be inspected separately.
PDB 1EHZ ↗Folded tRNA
Yeast phenylalanine tRNA, 1.93 Å. Its folded shape is reused as a generic tRNA in the teaching animation; the labels represent other tRNAs.
PDB 1BNA ↗DNA double helix
An experimental DNA dodecamer, 1.9 Å, in the molecule explorer. The animated DNA has an idealised helix and a custom teaching sequence.
What has been simplified?
The animation is a eukaryotic teaching model, not a reconstruction of one particular gene. DNA/RNA conformations and motion paths are idealised. Small-molecule chemical connectivity is generated with RDKit; hydrogen atoms, waters and charge states are omitted. The coloured overview representations are deliberately coarse.
Nucleotides are shown as ideal monophosphate units. Incoming triphosphates and pyrophosphate release are omitted. Translucent strand paths are backbone guides, not atom-resolved phosphodiester bonds; dashed pairing lines indicate complementarity, not calculated hydrogen-bond positions. Individual nucleotide geometry is detailed, but adjacent units are placed schematically. The close-up peptide has chemically connected atoms; its conformation is idealised.
RNA processing and export are summarised between views: introns are removed, exons joined, and mature mRNA leaves through a nuclear pore. The illustrated sequence is an 18-base coding-region excerpt, not a complete transcript. Promoters, untranslated regions, capping and polyadenylation machinery are not animated. A stop codon ends translation, not transcription.
Real tRNAs do not all have identical shapes or anticodons. The teaching anticodons show ideal complementarity; wobble is omitted. The initiator tRNA begins in the P site. During elongation the growing chain transfers to the A-site tRNA before translocation; no tRNA recognises a stop codon. A schematic release factor appears instead.
Initiation/elongation factors, tRNA charging enzymes and detailed energy coupling are omitted. Charging requires ATP, while key ribosomal steps use GTP. The peptide-transfer animation does not depict free amino acids condensing or ATP directly powering each peptide bond. A five-residue example is far shorter than a typical protein; its final fold is not predicted.
Cutaway hides front-facing parts of the machinery; it does not imply an actual opening. Colours, labels, enlarged close-ups and motion timing are for teaching. The growing chain uses a coral identity colour, a dark display outline and briefly pale newest residues. Clear view uses larger residue beads and quieter machinery colours; internal molecular geometry and the reaction sequence are unchanged. Attached chains are rigidly oriented away from their tRNA so they do not double back across its stem. The detailed close-up retains element colours. Chain close-up moves the camera only; it does not enlarge the chain relative to other molecules. Structure explorer preserves the downloaded complex coordinates after a rigid rotation/translation. Hydrogens, solvent and non-polymer ligands are normally hidden. The largest structure is sampled in software-rendering mode.
Keep a classroom copy
The illustrative animation works offline immediately. Actual macromolecules need an initial download. After loading them, save a self-contained copy.
No accounts, telemetry or installs.