Interactive 3D structural viewer for the human DNA Polymerase epsilon (Pol e) catalytic subunit (p261, UniProt Q07864).
This tool renders a procedural cartoon-ribbon schematic of the POLE holoenzyme directly in the browser using Three.js (WebGL). It is designed for exploring the domain architecture, catalytic mechanism, cancer-associated mutations, and clinical consequences of rare germline variants of Pol e.
Important: This is a schematic teaching model, not an atomic-coordinate viewer. The ribbon geometry, domain centers, and secondary-structure elements are procedurally generated to illustrate domain topology and functional relationships. Color modes (B-factor, conservation, charge, pathogenicity) display approximate domain-level or synthetic per-residue values, not crystallographic or computed data. For analysis of real atomic coordinates, load PDB 9F6D (Roske & Yeeles 2024, human Pol e-PCNA-DNA) into Mol* or PyMOL.
- Cartoon ribbon representation - helices, beta-strands (with arrowheads), and loops rendered per secondary structure element across all eight functional domains (NTD, EXO, Palm, P, Fingers, Thumb, Inactive-Pol, CTD)
- Two-metal-ion catalysis - ball-and-stick active site with octahedral Mg2+ coordination, conserved aspartate residues (D640, D642, D860), and distance annotations
- Incoming dNTP + Watson-Crick base pairing - template nucleotide with hydrogen bond visualization
- 3'-to-5' exonuclease site - two-metal proofreading active site with catalytic residues D275, E277, D368, D370
- Zinc-finger motifs - CysA/CysB Zn2+ tetrahedral coordination in the CTD
- [4Fe-4S] cluster - iron-sulfur cluster in the P domain (CysX motif), a feature unique to Pol e among B-family polymerases
- DNA double helix - template and primer backbone tubes with base-pair rungs
- Mutation hotspot markers - P286R, V411L, S297F, L424V, D287E, P436R, M444K, S459F, F367S with interactive tooltips
- Accessory subunits - ghost representations of POLE2 (p59), POLE3 (p17), POLE4 (p12)
- PCNA sliding clamp - toroidal processivity factor with homotrimer symmetry markers and tripartite Pol e contact interface (PIP-box Q1180, Thumb insertion res. 1102-1122, P-domain contact)
- Beta-sheet hydrogen bonds - inter-strand H-bond visualization (schematic, not from DSSP)
- Exo-Pol shuttling path - animated primer terminus transfer between active sites (~40 A, per Roske & Yeeles 2024)
| Mode | Description |
|---|---|
| Domain | Default domain-based coloring |
| B-factor | Approximate flexibility gradient by SS type (not crystallographic B-factors) |
| Conservation | Domain-level evolutionary conservation estimate (not per-residue MSA/ConSurf) |
| Variant | COSMIC/ClinVar variant density (domain-level approximation) |
| Charge | Amino acid formal charge (domain-level average, not APBS electrostatics) |
| Pathogenicity | Clinical significance spectrum (blue-green = benign, white = VUS, red = pathogenic) |
- Default - muted, publication-quality palette
- PyMOL - classic PyMOL-style bright colors
- Accessible - colorblind-friendly palette
A separate page (molstar.html) provides a real coordinate viewer using Mol*, the same viewer used by RCSB PDB and PDBe. Features:
- Loads PDB 9F6D (Roske & Yeeles 2024) with domain-colored cartoon representation
- Finger conformational triad: switch between open (9F6D), ajar (9F6E), and closed (9F6F) states
- PDB 9B8S (He et al. 2024) — independent Pol e-PCNA cryo-EM structure
- Real DSSP secondary structure, crystallographic B-factors, metal coordination geometry
- Multiple representations: cartoon, ball-and-stick, surface, putty (B-factor), spacefill
- Domain coloring, chain coloring, element coloring, secondary structure coloring
- Toggle Mol* built-in controls for advanced operations
A variant analysis page (variant.html) provides per-mutation analysis for all characterized POLE pathogenic variants:
- ACMG classification with Bayesian posterior probabilities (Mur et al. 2023 framework)
- Auditable evidence codes — each PS/PM/PP code has a literature citation
- Mutational signature attribution — per-variant SBS10a/b/28/14 weights with bar charts
- DDG stability prediction — heuristic destabilization estimate (not FoldX/Rosetta)
- Mol structural context* — variant residue highlighted in PDB 9F6D coordinates
- URL-addressable variants:
variant.html#P286R,variant.html#V411L, etc.
A separate page (mutation.html) visualizes the ultra-rare c.138del germline variant (p.Leu46Phefs*8), showing:
- Side-by-side wild-type vs. truncated mutant comparison
- Domain retention bar chart (54 / 2,286 residues = 2.4% translated)
- Reading frame analysis with frameshift coloring
Clinical note: truncating POLE variants such as c.138del are typically classified as likely benign for polymerase-proofreading-associated polyposis (PPAP). PPAP requires an active but proofreading-deficient polymerase to generate a mutator phenotype; a null allele (as produced by early frameshift) does not confer a mutator effect, and the wild-type allele provides sufficient function. See Mur et al. 2023 for the gene-specific ACMG/AMP classification framework.
A Julia data pipeline (pipeline/) computes variant scoring, mutational signature deconvolution, Bayesian variant classification, and structural math from PDB coordinates, outputting JSON consumed by the viewer at runtime. See pipeline/README.md for details. When pipeline JSON is unavailable, the viewer falls back to built-in default values.
Serve the project directory with any static HTTP server:
npx serve .Then open http://localhost:3000 in a modern browser.
| Input | Action |
|---|---|
| Drag | Orbit camera |
| Shift+Drag | Pan |
| Scroll | Zoom |
| Hover | Inspect elements (tooltip) |
1-8 |
Focus domain |
R |
Toggle auto-rotate |
S |
Screenshot (PNG) |
M |
Measure distance |
H |
Toggle helix H-bonds |
B |
Toggle beta-sheet H-bonds |
Z |
Toggle Zn-finger motifs |
P |
Toggle PCNA clamp |
D |
Toggle DNA |
L |
Toggle labels |
E |
Toggle Exo-Pol path |
? |
Keyboard shortcuts |
This viewer is a schematic teaching tool, not a molecular graphics program:
- Coordinates are procedural. Ribbon paths are generated algorithmically to approximate domain topology, not parsed from PDB ATOM records. Domain centers are hand-placed to reflect the spatial arrangement in the Roske & Yeeles 2024 structures but are not superimposed on deposited coordinates.
- B-factors are not crystallographic. The B-factor color mode assigns a single pseudo-value per secondary-structure type (helix = 0.2, strand = 0.5, loop = 0.9). Real B-factors require a refined coordinate set.
- Conservation is domain-level. Values are literature-derived per-domain estimates, not per-residue Shannon entropy from a multiple sequence alignment. For real per-residue conservation, use ConSurf with UniProt Q07864.
- Electrostatic surface is not computed. The charge mode shows formal amino acid charge averaged per domain, not a Poisson-Boltzmann (APBS/PDB2PQR) electrostatic potential mapped onto a solvent-excluded surface.
- The molecular envelope is a geometric approximation, not a Connolly/MSMS solvent-excluded surface.
- H-bonds are schematic. They are placed along the backbone to illustrate i->i+4 and inter-strand patterns, but donor-acceptor distances and angles are not computed from atomic coordinates via DSSP.
For coordinate-derived molecular visualization, load PDB 9F6D (human Pol e-PCNA-DNA, open Finger conformation) into Mol* or PyMOL.
- UniProt Q07864 (POLE_HUMAN)
- PDB: 9F6D, 9F6E, 9F6F (Roske & Yeeles 2024); 9B8S (He et al. 2024); 4M8O (Hogg et al. 2014)
- Roske & Yeeles, Nat Struct Mol Biol 31:1921-1932 (2024) — first human Pol e catalytic domain structures: open (9F6D), ajar (9F6E), and closed (9F6F) Finger conformations; four mismatch proofreading intermediates (post-insertion, arrest, frayed substrate, mismatch excision)
- He, Wang, Yao, O'Donnell & Li, Nat Commun 15:7847 (2024) — independent human Pol e-PCNA cryo-EM structure (9B8S)
- Mur, Viana-Errasti et al., Genome Med 15:85 (2023) — gene-specific ACMG/AMP framework for POLE/POLD1 germline variant classification with likelihood-ratio-based Bayesian update
- Yuan, Georgescu, Schauer, O'Donnell & Li, Nat Commun 11:3156 (2020) — yeast Pol e holoenzyme structure revealing the non-catalytic Pol2 module
- Robinson, Coorens et al., Nat Genet 53:1434 (2021) — normal-tissue somatic mutation rates in POLE/POLD1 germline carriers (Sanger)
- Hogg, Osterman, Goldsmith et al., Nat Struct Mol Biol 21:49-55 (2014) — S. cerevisiae Pol2 catalytic domain (4M8O)
Apache 2.0 — see SECURITY.md for vulnerability reporting.