Anthropic Says Claude Helped Map the First 3D Structure of a Bacterial Vault

Vaults were discovered in 1986 and have been studied mainly in mammalian cells, where the shell is built from 78 copies of a single protein. The structure Anthropic's team mapped, which it calls L05, comes from a bacteriophage, a virus that infects bacteria. It is built from 96 copies of one phage protein, has a combined mass of about 9.5 megadaltons and encloses roughly 25% more volume than its mammalian counterpart despite being shorter, because it is more spherical.

What Claude Did

The company describes the model's role as substantial but supervised. Using a tool it calls Claude Science, the model searched a database of about 15 billion predicted proteins and found vault relatives across 29 bacterial and four archaeal phyla, present in under 1% of species with sequenced genomes. It helped select candidate proteins for testing, converted their sequences into host-tailored DNA and prepared orders. Of 24 proteins moved into E. coli, 15 produced soluble protein and seven formed vault-like particles, four of which were confirmed by cryo-electron microscopy.

Claude also proposed a faster purification method that loads ruptured-cell contents directly onto a chromatography column, cutting a step that normally takes about three days to roughly 90 minutes. It ran the structural processing in an internal multi-agent system, producing a first model in 34 hours and final maps about a week after processing began. Anthropic said the whole project took under four months, and that the model flagged an unidentified small molecule sitting in a pocket in each of the 96 protein copies, with a shape resembling coenzyme A.

Where It Went Wrong

Anthropic was candid about the errors. A protocol Claude wrote included a growth-medium additive that interferes with DNA uptake, costing about two weeks. Early cryo-EM processing skipped a standard step and produced a flawed map blended with its mirror image, which human researchers caught. The team told the model, in its words, "Please let's do normal things unless they don't work." Humans directed the research, made analysis decisions and judged the results throughout.

The work was advised by Leonard Rome, who co-discovered vaults in 1986 and served as a paid consultant. "Figuring out the function of vaults is still enormously challenging," he said. The authors cautioned that the particles were made only in E. coli, so whether they form in their native bacteria and phages is untested, and the biological purpose of vaults remains unknown.

The release is the latest in a push by AI labs to show their models producing original scientific results rather than summarising existing knowledge. Anthropic has said it will release the structures and underlying data, and listed two of the paper's authors as contacts for research collaborations.