Learn/Predict a structure
Start with the sequence
Transferrin receptor 1 sits on the surface of most human cells and carries iron in, bound to transferrin. It is abundant on the cells that line the brain's blood vessels, which is why it is the receptor that drug and gene-delivery binders are aimed at to cross into the brain. A binder campaign against it starts with its structure, and the structure a binder sees is the part outside the cell: the ectodomain.
The receptor is 760 residues long, but only the ectodomain is in the crystal structures. The cytoplasmic tail and the transmembrane helix at the start of the chain would fold as low-confidence noise and slow the run. Residues 122 to 760 are the input; the rest is trimmed before anything is submitted.
Transferrin receptor protein 1, full length
Highlighted: the ectodomain, 639 residues, the chain of 1CX8 that every later step folds.
Barnase with barstar
Barnase · chain A · 110 residues
Barstar · chain B · 89 residues
Two chains are a complex: in the Structure lab they are two rows, or one sequence with a colon between them. The model is asked where they sit against each other as well as how each folds.
A row is a protein, DNA or RNA, or a ligand
- Protein
- One chain per row, or several joined with a colon. Every folding model takes it.
- DNA, RNA
- Nucleic acid chains. Boltz-2 and OpenFold 3 fold them with the protein.
- Ligand
- A small molecule as SMILES or a CCD code. Boltz-2 and OpenFold 3 place it; Boltz-2 can also estimate its affinity.
Do this in Phi
Open the Structure lab. Paste the ectodomain sequence into Sequence, or drop a FASTA file on it. For the complex, add a second Protein row or join the chains with a colon.
Read more: UniProt P02786 · PDB 1CX8