ACTR1A (Arp1): nucleotide site and polymerisation interface

Generated by analyze_arp1_actin_fold.py (uv run python analyze_arp1_actin_fold.py). Overwritten on every run; do not hand-edit.

Sequences: ACTB P60709 (375 aa), ACTR1A P61163 (376 aa), ACTR1B P42025 (376 aa), ACTR10 Q9NZ32 (417 aa)

A. Actin's ATP site, transferred by alignment

Reference: PDB 2BTF chain A (BETA-ACTIN, source organism Bos taurus, 99.7% identical to human ACTB over the modelled region), ligand ATP, heavy-atom cutoff 4.5 A. Nucleotide-contacting residues found from coordinates: 25. The reference is not human, so contacts are transferred through human ACTB rather than read off directly.

* = residue differs from beta-actin at that position.

B. What the human dynactin structure actually models

PDB 9B85 chain inventory:

• ACTR1A protomers modelled: 8 (chains A, B, C, D, E, F, G, I); the modelled sequence is 100.0% identical to UniProt P61163.
• ACTR1A chains with a modelled nucleotide: 8/8, ligand(s) ADP.
• Residues within 4.5 A of that nucleotide: 22 positions across protomers, 15 of them in every protomer.
• Of those positions, 20 align onto residues that contact ATP in 2BTF beta-actin, i.e. the ACTR1A nucleotide sits in the conserved actin nucleotide cleft.

C. Who polymerises and who terminates

Inter-chain heavy-atom contacts (cutoff 4.5 A) among the filament chains of 9B85:

Largest ACTR1A-ACTR1A interface: chains E-G, 265 atom contacts over 21 ACTR1A residues. In beta-actin numbering these span 38-245, of which 14 lie N-terminal to actin residue 70 (subdomain 2, the DNase-I-binding loop that makes actin's longitudinal filament contact): [38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 61, 62, 63, 64].

Full ACTR1A interface residue list for that pair (P61163 numbering, nothing omitted): 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 65, 66, 67, 68, 205, 209, 213, 243, 244, 245, 246. The subdomain-2 residues are the ones that carry the polymerisation argument; the higher-numbered positions are subdomain-3/4 contacts on the partner face and are reported here for completeness.

Generalising beyond that single pair: splitting the ACTR1A-ACTR1A interfaces at the largest gap in their contact counts separates 6 large (>= 230 atom contacts, intra-protofilament) interfaces from the smaller lateral ones. Positions present in every large interface: 44, 45, 46, 47, 48, 49, 51, 52, 65, 66, 67, 68, 205, 213, 243, 244, 245, 246. In beta-actin numbering, those below residue 70 (subdomain 2) are [40, 41, 42, 43, 44, 45, 47, 48, 61, 62, 63, 64] and the rest are [200, 208, 242, 243, 244, 245].