ACTR10 (Q9NZ32) bioinformatics

Generated by uv run python analyze.py on 2026-07-26. Five questions are addressed.

1. Where did ACTR10's phylogenetically-propagated (IBA) annotations come from, and
   what does each source actually know? (paint_sources.py)
2. Does ACTR10 still have a working actin nucleotide site, and has it lost the
   actin polymerisation interface? (nucleotide_site.py)
3. Do the nuclear and dynactin actin-related proteins localise differently in one
   human dataset? (nuclear_arp_control.py)
4. Is the missing nucleotide-binding annotation peculiar to ACTR10, and which term do
   GO curators actually use for the actin-fold nucleotide site?
   (nucleotide_gap_survey.py)
5. Do the other dynactin subunits share ACTR10's granule/extracellular annotations?
   (subunit_granule_survey.py)

All input is fetched live from UniProt, QuickGO, RCSB and the Human Protein Atlas at
run time.

PAINT (IBA) source resolution and source-side evidence

Built directly from ACTR10-goa.tsv column WITH/FROM; token counts are asserted against the file. own evidence is what QuickGO reports for that source protein on the propagated term or its is_a/part_of descendants. Experimental codes counted: EXP, HDA, HEP, HGI, HMP, HTP, IDA, IEP, IGI, IMP, IPI.

GO:0005634 nucleus (cellular_component, is_active_in, IBA)

5 WITH/FROM tokens.

• protein sources: 4; with own experimental evidence for this term: 4; with a reviewed (Swiss-Prot) record: 2

GO:0005869 dynactin complex (cellular_component, part_of, IBA)

4 WITH/FROM tokens.

• protein sources: 3; with own experimental evidence for this term: 3; with a reviewed (Swiss-Prot) record: 2

GO:0005200 structural constituent of cytoskeleton (molecular_function, enables, IBA)

11 WITH/FROM tokens.

• protein sources: 10; with own experimental evidence for this term: 10; with a reviewed (Swiss-Prot) record: 10

GO:0098958 retrograde axonal transport of mitochondrion (biological_process, involved_in, IBA)

2 WITH/FROM tokens.

• protein sources: 1; with own experimental evidence for this term: 1; with a reviewed (Swiss-Prot) record: 0

IPI (GO:0005515 protein binding) partners

A. Is a nucleotide modelled in Arp11, and in its neighbours?

All 24 PDB entries whose UniProt mapping contains human ACTR10 (Q9NZ32) or pig ACTR10 (I3LHK5). Within each entry the Arp1 and beta-actin chains are the internal control: they are the polymerising actin-fold subunits of the same filament, imaged in the same experiment.

Entries in which a nucleotide is modelled in the Arp11 chain: 5AFU (ADP), 6F1T (ADP), 6F38 (ADP), 6F3A (ADP), 6ZNL (ADP), 6ZNM (ADP), 6ZNN (ADP), 6ZNO (ADP), 6ZO4 (ADP), 7Z8F (ATP), 7Z8M (ATP), 8PR4 (ATP), 8PTK (ATP), 9DGS (ADP), 9DGT (ADP), 9DGU (ADP), 9DGV (ADP), 9HHL (ATP), 9YNG (ADP)

Split by ligand modelled in the Arp11 chain: ADP in 14 entries; ATP in 5 entries (of 24 entries surveyed, 5 model no nucleotide in that chain).

B. Nucleotide contacts computed from 7Z8M coordinates

Every residue with a heavy atom within 4.0 A of a nucleotide in the same chain, computed from the deposited model.

C. Are the contacts conserved in human ACTR10?

Pig ARP10 (I3LHK5, 417 aa) vs human ACTR10 (Q9NZ32, 417 aa): 400 identical aligned positions (95.9% of the shorter sequence). The structure is pig, so every contact is transferred through this alignment.

17/18 of the pig Arp11 ATP-contacting residues are identical in human ACTR10.

Human beta-actin (P60709, 375 aa) vs human ACTR10: 105 identical aligned positions (28.0% of actin). ACTR10 is the most divergent member of the family, so this alignment is included to locate actin's own nucleotide site, not to claim close homology.

9/17 of beta-actin's own ADP-contacting residues are identical in human ACTR10; 0/17 fall in an alignment gap.

Test of the subdomain-2 loop deletion (Eckley et al. 1999)

Eckley et al. 1999 predicted that Arp11 lacks actin residues 38-57, the subdomain-2 surface loop on the pointed-end face, and that this is why Arp11 cannot be polymerised past. In the alignment above, 20/20 of actin positions 38-57 align to a gap in human ACTR10.

ACTB   VFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILT
ACTR10 IIPSVIKR--------------------AGMPKPVRV

D. Nuclear versus dynactin actin-related proteins in one human dataset

The GO:0005634 nucleus IBA on ACTR10 is propagated from nuclear ARPs of another subfamily (Arp9, Actl7a). If that subfamily split is real, then in human the nuclear ARPs and the dynactin ARPs should localise differently. Human Protein Atlas immunofluorescence is queried for both clades plus conventional actin. Antibody-based localisation is one line of evidence, not proof; it is used here only as a reciprocal control.

• nuclear-ARP clade: 3/4 genes with a nuclear compartment in their HPA location list (ACTL6A:nuclear, ACTL6B:nuclear, ACTR6:non-nuclear, ACTR8:nuclear)
• dynactin clade: 0/3 genes with a nuclear compartment in their HPA location list (ACTR10:non-nuclear, ACTR1A:non-nuclear, ACTR1B:non-nuclear)
• excluded from those denominators because HPA reports no location: ACTB (conventional actin) - HPA record present but no location reported; ACTR5 (nuclear ARP (INO80)) - HPA record present but no location reported
• clade sizes in the panel before exclusions: nuclear-ARP clade 5; dynactin clade 3

E. Nucleotide-binding annotation across the actin-fold family

QuickGO annotations under GO:0000166 nucleotide binding (descendants included) for a panel of actins and actin-related proteins. This asks whether ACTR10's missing nucleotide term is peculiar to ACTR10, and which term GO curators actually use for the actin-fold nucleotide site.

• 2/12 panel members carry any nucleotide-binding annotation (ACTA1, ACT1)
• 10/12 carry none (ACTB, ACTG1, ACTR1A, ACTR1B, ACTR2, ACTR3, ACTR10, ARP10, ACTL6A, ACTR8)
• GO:0005524 ATP binding: ACTA1, ACT1
• GO:0043531 ADP binding: ACTA1

F. Granule and extracellular annotation across the dynactin subunits

QuickGO annotations to the three terms removed from ACTR10 in this review, across the 11 canonical dynactin subunits named in UniProt's SUBUNIT line for Q9NZ32, plus ACTR1B scored separately as a twelfth protein. Evidence codes are shown because a Reactome TAS term and an HDA mass-spectrometry term are different artefact classes.

• canonical subunits carrying any of the three terms by any evidence code: 3/11 (ACTB, CAPZA1, ACTR10)
• canonical subunits carrying any of the three terms by Reactome TAS: 2/11 (CAPZA1, ACTR10)
• canonical subunits annotated to GO:0035578 azurophil granule lumen: 1/11 (ACTR10)
• canonical subunits whose Reactome TAS comes from the Neutrophil degranulation route: 1/11 (ACTR10)
• outside the canonical 11, on the Neutrophil degranulation route: ACTR1B

Reactome reactions behind the TAS annotations above: