× MODEL NOTES & SOURCES
An atlas, not a diagnosis. This WebGL explorer uses detailed procedural surfaces, membranes, folded sheets, tubes and sampled molecular particles to explain cellular anatomy. It does not reconstruct an individual cell, simulate biochemical kinetics, or predict whether a mutation causes cancer. Fine structures are schematic; no atomic structures are loaded.
How the mutation lab works The featured TP53 Y163C switch represents a specific missense variant; the other three switches represent activating KRAS, RB1 loss and PTEN loss. These are not equivalent to every variant in those genes. They highlight relevant locations and change qualitative pathway explanations. They do not calculate mutation penetrance, growth rate or cancer risk.
The morphology option is independent. The guided story is an authored teaching sequence, not a typical order or timescale of cancer development. Cilia and stress structures are optional, cell-dependent teaching overlays. The metaphase scene suppresses nuclear envelope, nucleolus and interphase chromatin displays.
How to read the detail Geometry represents selected cellular structures, not every protein, RNA, ion or metabolite. Protein complexes are enlarged morphology symbols. Positions, counts, textures and colors are authored, not measured. The generic interphase cell is not a reconstruction of one tissue or cell line.
Conditional overlays include stress granules, glycogen, paraspeckles, microvilli, cilia and division structures. Showing all overlays together does not describe a single physiological state. Electron-image-inspired · gray is a rendering style, not simulated electron microscopy.
Motion and transport Cell Motion uses a repeating illustrative trajectory. The channel activity overlays show selected transport mechanisms with assumed gradients. Their speeds, ion paths and cell movements are authored for teaching.
Implemented in this version 59 structure groups with independently switchable sublayers; shaded WebGL geometry; orbit and zoom; adjustable section depth; five peel stages; paginated exploded components; organelle close-ups; opacity and detail controls; component inspection and isolation; baseline comparison; TP53 Y163C and three other functional-alteration scenarios; saved and exportable configurations. Molecular symbols are representative. Predictive simulation, measured cell geometry and atomically resolved proteins remain future work.
× VARIANT SPOTLIGHT / TP53
One residue. A different structure. Y163C · p.Tyr163Cys · NM_000546.6:c.488A>G
WILD-TYPE RESIDUE Y 163 Tyrosine CH₂–C₆H₄–OH
MUTANT RESIDUE C 163 Cysteine CH₂–SH
What the evidence supports ClinGen’s TP53 expert panel reports impaired transactivation and growth-suppression activity in functional assays. Its pathogenic classification is for germline Li-Fraumeni syndrome; that classification does not mean every cell carrying this change is cancerous.
Structural research identifies destabilisation and a flexible mutation-associated pocket. PDB 8QWL is a 1.65 Å X-ray structure of the Y163C p53 DNA-binding-domain construct. It is not an entire p53 tetramer or a whole-cell structure. These cards explain the substitution; they are not atomic models.
The cell overlay marks the affected p53 regulatory system. It does not calculate pocket geometry, drug binding, rescue efficacy or cancer risk. A mutation-associated pocket is a research opportunity, not proof of an effective treatment.
× WHY THIS MODEL EXISTS
Connect cell structure to cell function. This is an interactive biology learning and mechanism-exploration tool. Explore how a membrane maintains gradients, how DNA is packaged, and how impaired p53 function can weaken cancer-protective responses. It is not a game, a digital replica of one person’s cell, or a validated predictor of malignant transformation.
What Y163C changes The mutation changes TP53 coding nucleotide c.488A>G, replacing Tyr163 with cysteine. The pathway view contrasts the normal p53 response with reported loss of transcriptional and growth-suppression function. Other cellular changes are context dependent; toggling Y163C does not justify inventing a specific tumor shape, division rate, chromosome count or ion flux.
Colors and motion Most unstained cell structures are weakly colored and transparent in ordinary light microscopy. Molecular detail is below optical resolution. Fluorescence colors depend on labels; electron micrographs do not record visible-light color. The biology palette distinguishes components; neutral and grayscale materials are illustrative alternatives, not true-color microscopy.
Ion and molecule tracers use enlarged symbols and slowed playback. The pump preserves the 3 Na⁺ out / 2 K⁺ in ratio per ATP cycle. Channel directions assume stated gradients. Gate, ATP and pause controls demonstrate mechanisms; they do not calculate current, membrane voltage, kinetics or disease physiology.
Biology coverage audit System Implemented representation Remaining limit Membrane Leaflets, lipids, sterols, pumps, channels, aquaporin, GLUT, flippase / scramblase Selected families; no complete proteome or atomic coordinate fit Genome Antiparallel DNA, A–T / G–C pairs, histone octamer, wrapped and linker DNA, 46 replicated chromosomes No complete genome sequence or measured chromosome territories Organelles Nuclear envelope, ER, Golgi, mitochondrial membranes / cristae, degradative and trafficking compartments Authored positions and abundance; tissue-specific differences remain Cell dynamics Ion transport, water / glucose passage and p53 pathway playback No reaction–diffusion, electrophysiology or validated kinetic simulation Cancer Evidence-linked Y163C function; other defined alteration overlays No patient-specific cancer prediction or drug-rescue calculation
What does a real cell look like? Most unstained mammalian cell contents have little visible color. Brightfield and phase imaging show contrast from the specimen and optics; fluorescent labels and electron-image colorization do not establish natural organelle colors. This model keeps tiny structures visible through enhanced relief, so none of its modes is a simulated microscope acquisition.
Allen Institute: actual brightfield images and label-free prediction · Compare brightfield inputs with predicted, colored structures
Research anchors