UniProt Q9H9F9 · HGNC:14671 · 607 aa · PE 1: Evidence at protein level ·
chromosome 20 · MIM 619730.
Reviewed as part of the PAINT + affinage campaign. Sibling actin-family reviews
already merged: ACTB, ACTL7A, ACTL7B, ACTL8, ACTR1A, ACTR1B, ACTR10. A parallel
agent may be reviewing ACTR8 (the other actin-related INO80 subunit); the
differences between ACTR5 and ACTR8 are set out under
"Where ACTR5 and ACTR8 differ" below.
ARP5 is one of two actin-related proteins in the human INO80 chromatin-remodelling
complex. It is not a cytoplasmic actin: it is a nuclear ARP, and it sits in
INO80's catalytic C-module together with the Ino80 Snf2 motor, IES6/INO80C,
IES2/INO80B and the RuvBL1–RuvBL2 heterohexamer
PMID:41775336.
Human subunit mapping placed it there in 2011
PMID:21303910,
and the same study showed that catalysis requires the full conserved subunit set
PMID:21303910.
hARP5 is predominantly nuclear but shuttles
PMID:19014934,
and it complements a yeast arp5Δ
PMID:19014934 —
i.e. the ARP5 function is conserved from yeast to human, which is the biological
warrant for the phylogenetic (IBA) annotations discussed in §4.
This is the headline finding of the review.
ACTR5's GOA molecular-function record consists of exactly two things: one IBA to
GO:0030234 enzyme regulator activity, and fourteen rows of bare
GO:0005515 protein binding. There is no DNA-binding, nucleosome-binding,
chromatin-binding or nucleotide-binding annotation of any kind — even though
the mechanism has been resolved structurally in the human complex.
What the structures show. In the 2018 human INO80–nucleosome map the ARP5–IES6
module contacts the nucleosome on the face opposite the motor domains
PMID:29643506,
at SHL −2/−3
PMID:29643506.
The 2026 higher-resolution states identify the contacting element and the chemistry:
PMID:41775336
and
PMID:41775336.
So ARP5's contact is sequence-independent nucleosomal DNA binding, i.e.
GO:0031492 nucleosomal DNA binding (which is_a GO:0031491 nucleosome binding,
is_a GO:0003677 DNA binding, is_a GO:0003682 chromatin binding, so the single
specific term subsumes all three).
Why the qualifier must be contributes_to rather than enables: the isolated
protein does not bind nucleosomes at physiological concentration without IES6
PMID:29643506.
The functional unit is the ARP5–IES6 module.
Why it matters mechanistically: the module is the anchor that converts the Ino80
motor's ATP turnover into directional nucleosome translocation
PMID:29643506,
PMID:29643506.
In yeast the same conclusion is reached from the opposite direction — adding back
the module restores both ATPase and sliding, whereas an insertion-domain deletion
uncouples them
PMID:26306040,
PMID:26306040,
and the 2025 yeast study states the role directly
PMID:39676660.
Consequence for GO:0030234. The vague parent should be replaced by two
informative terms: GO:0060590 ATPase regulator activity (exactly what the
donor's own IDA measured — modulation of an ATP hydrolysis activity) and, with
contributes_to, GO:0140658 ATP-dependent chromatin remodeler activity (the
activity of the machine ARP5 is an obligate part of).
The hierarchy here was checked in QuickGO and confirmed in OLS, and the first
version of this review got part of it wrong — corrected after review of #2291:
| term | its only is_a parent |
descendant of GO:0030234? |
|---|---|---|
GO:0060590 ATPase regulator activity |
GO:0060589 nucleoside-triphosphatase regulator activity |
yes, two steps down — not a direct child, as originally written |
GO:0060589 |
GO:0030234 |
yes, directly |
GO:0001671 ATPase activator activity |
GO:0140677 molecular function activator activity |
no |
So GO:0001671 really is outside the GO:0030234 branch (the reviewer's guess
that it sits under GO:0060590 is not what either ontology service reports —
GO:0060590's single is_a child is GO:0000774 adenyl-nucleotide exchange
factor activity), but GO:0060590 is a grandchild rather than a child, and
naming both GO:0140677 and GO:0098772 as GO:0001671's parents was
redundant since GO:0140677 is_a GO:0098772.
GO:0001671 is now named as the available alternative rather than dismissed:
it is the term the yeast add-back licenses, and a curator who weights
PMID:26306040's explicit stimulation result above the human coupling data should
use it. This review prefers the direction-neutral GO:0060590 because the yeast
result is an ectopic reconstitution add-back of the whole module, and because in
human INO80 the mutations that break the ARP5/IES6-side nucleosome contacts lose
sliding while retaining robust ATPase — so what the human evidence isolates is
coupling, not stimulation.
ACTR5-bioinformatics/ACTR5-bioinformatics/nucleotide_site.py → results.json → RESULTS.md
(regenerating reproduces the committed report byte-for-byte; four deliberate
break-tests confirm the guards fire). Full numbers in
file:human/ACTR5/ACTR5-bioinformatics/RESULTS.md.
Positive direction — a nucleotide really is there, in the actin site. ADP is
modelled inside the ARP5 chain in 3 of the 6 human INO80 depositions
(7ZI4 3.2 Å, 9GCG 3.43 Å, 9GE5 3.35 Å; 12–16 ARP5 residues within 4.0 Å); ATP
never is. The ARP5 chain is identified from the PDBe SIFTS UniProt mapping, so a
missing Q9H9F9 mapping aborts the run rather than producing a silent zero.
The reciprocal test — do ARP5's observed contacts land on positions that
align to β-actin's own ATP contacts in 2BTF? — gives 13/16, 11/14 and 8/12
(0.81 / 0.79 / 0.67). The retained contacts are actin's two phosphate-binding
loops (ACTB G13-S14-G15-M16-K18 → ACTR5 G38-S39-F40-Q41-R43; ACTB G156 → ACTR5
G189) and the adenosine shelf (ACTB G302/M305/Y306 → ACTR5 G496/M499/Y500). This
is the canonical actin cleft, not an adventitious surface site.
Every one of those depositions was prepared with ADP·BeF3
PMID:41775336,
which would ordinarily leave the identity of the ligand ambiguous. It does not
here, and this was computed rather than argued (added after review of #2291,
which asked exactly the right question): in all three entries the ARP5 chain
contains no BeF3, AlF, VO4 or PO4 group alongside its ADP, and in 7ZI4 the only
BeF3 in the whole entry sits in chain G, the Ino80 motor — which is where an
ATP mimic belongs. The soak therefore qualifies what the motor was trapped
with, not what ARP5 holds. What the structures still cannot do is rank ADP
against ATP, because no ATP was offered to ARP5 in solution; that limitation
stays in knowledge_gaps. GO:0043531 ADP binding follows the campaign's stated
rule ("annotate the ligand actually observed") and matches ACTR1A/ACTR1B.
Resolutions in the report are now the PDBe-reported values, fetched rather than
transcribed (6HTS 4.8, 7ZI4 3.2, 9GCG 3.43, 9GE5 3.35, 9GEV 3.47, 9GFB 3.55 Å).
These differ from the "3.5–3.7 Å" figures the 2026 paper quotes, which are its
own overall map resolutions for the nucleosome/hexasome states; both are
correct and the review now says which is which rather than mixing them.
Negative direction — no ATPase, no filament. Of the five literature-defined
actin catalytic positions (ACTB D11/Q137/D154/V159/H161, the same set the ACTL7A
audit used), ACTR5 keeps 2/5: DDSCH. Asp11 and His161 are retained but
Gln137 — which orients the attacking water — plus Asp154 and Val159 are not. So
the pocket binds while the hydrolysis machinery is degenerate; no ATPase term is
warranted, and GOA asserts none. Independent corroboration: the already-merged
genes/human/ACTL7A/ACTL7A-bioinformatics/results.json computes the identical
string DDSCH for ARP5_HUMAN, and this script hard-fails on disagreement.
On the F-actin protomer interface (8A2S, 72 consensus positions) ACTR5 retains
20.8% identity, against 51.4% for ARP1/ACTR1A — the one ARP that really
does polymerise, used here as the positive control — and 100%/94.4% for
ACTB/ACTA1. A 2.5-fold gap, unchanged under BLOSUM45 with a (−14,−2) gap model
(18.1%). ACTR5 cannot be expected to polymerise, and GOA correctly carries no
actin-binding, actin-filament or protein-polymerisation term.
No cytoplasmic-actin leakage. This was checked explicitly, in both of the
directions this campaign has been burned by. ACTL8's defect was a divergent actin
placed inside PANTHER's cytoplasmic β/γ-actin subfamily; ACTR10's was a
GO:0005634 nucleus IBA transferred from nuclear ARPs of a different
subfamily. Neither shape applies here: every resolvable WITH/FROM donor on every
ACTR5 IBA row is an ARP5 ortholog (§4), and ACTR5's nuclear localisation is
its own (three IDAs plus one EXP), not a transfer. The only cytoplasmic claim in
the record is ACTR5's own documented shuttling — see §5.
Five PAN-GO IBA rows, GO_REF:0000033, all at PANTHER node PTN000233752
inside the pan-actin family PTHR11937. Accessions resolved with
size=2+ queries and primaryAccession == requested as the liveness guard:
| WITH/FROM token | resolves to | status | name |
|---|---|---|---|
FB:FBgn0038576 |
Q9VEC3 (+ TrEMBL duplicate A0A0B4KG83, same gene, same name) | Swiss-Prot | Actin-related protein 5, D. melanogaster |
SGD:S000005004 |
P53946 | Swiss-Prot | Actin-related protein 5, S. cerevisiae |
PomBase:SPBC365.10 |
Q9Y7X8 | Swiss-Prot | Actin-like protein arp5, S. pombe |
AGI_LocusCode:AT3G12380 |
Q940Z2 | Swiss-Prot | Actin-related protein 5, A. thaliana |
UniProtKB:Q9H9F9 |
self | Swiss-Prot | ACTR5 — a self-referential IBA, i.e. a PAINT curator judging the function core |
PANTHER:PTN000233752 |
internal tree node, not a protein | — | — |
This is the cleanest donor set the campaign has seen: five for five reviewed
Swiss-Prot ARP5 orthologs, zero paralogs, zero unreviewed entries. Contrast
ACTL8, where the node's other members were β-actin at ≥90% identity.
Donor evidence for the term each donated (QuickGO, goUsage=descendants,
experimental codes EXP/IDA/IPI/IMP/IGI/IEP/HTP/HDA/HMP/HGI/HEP):
| term | donors | each donor's own experimental evidence |
|---|---|---|
GO:0006338 chromatin remodeling |
fly, pombe, yeast, self | fly IMP (PMID:16618800); pombe IDA (PMID:19933844); yeast IDA ×3 + IMP ×2 + IPI; self IDA (PMID:21303910) |
GO:0031011 Ino80 complex |
fly, pombe, yeast, self | fly IDA+IPI; pombe IDA+IPI; yeast IDA ×2 + IMP + IPI ×2 |
GO:0006355 reg. of DNA-templated transcription |
fly, self | fly IMP (PMID:16618800); self IMP via GO:0045893 |
GO:0030234 enzyme regulator activity |
yeast | yeast IDA (PMID:26306040) |
GO:0005737 cytoplasm |
Arabidopsis, self | Arabidopsis IDA (PMID:19679120); self IDA (PMID:19014934) |
Every donor carries its own experimental evidence for the term it donated. So
SOURCE_WEAK_OR_INFERRED / SOURCE_EVIDENCE_WEAK are factually excluded here,
and no row was dismissed on source-quality grounds. The only propagation defects
found are (a) a qualifier that over-reaches (§5) and (b) a term the node holds
but never propagated (§6).
The bioinformatics panel adds that the four donor orthologs sit in the same
structural regime as human ARP5 — partly conserved nucleotide pocket (33–39%),
degenerate filament interface (15–22%), 1–2/5 catalytic positions — so the
nucleotide site and the loss of polymerisation competence are family-wide ARP5
properties, not human peculiarities.
is_active_in cytoplasmGO:0005737 cytoplasm reaches ACTR5 three times: an IBA with
is_active_in, an IEA from UniProtKB-SubCell:SL-0086, and an IDA from
PMID:19014934, all located_in except the IBA.
The term is right. hARP5 genuinely visits the cytoplasm — that is the
gene's own finding
PMID:19014934 —
and UniProt records Cytoplasm {ECO:0000269|PubMed:19014934} with the note that
the protein is predominantly nuclear. The donor is equally sound: Arabidopsis
ARP5 has its own cytoplasm IDA.
The qualifier is not. is_active_in asserts that the gene product carries out
its molecular function in that compartment. Every characterised ARP5 activity —
nucleosomal DNA binding, INO80 C-module assembly, chromatin remodelling, the DNA
repair phenotypes — is nuclear; nothing has been shown for the cytoplasmic pool
beyond its existence in transit. Recorded as MARK_AS_OVER_ANNOTATED with
root_cause: TERM_SCOPING_PROBLEM (whose definition explicitly covers a wrong
qualifier) and a PAINT recommendation to change is_active_in → located_in at
node PTN000233752. The located_in rows are kept.
Budding-yeast ARP5 (SGD:S000005004, P53946) — a WITH/FROM donor on four of the
five ACTR5 IBA rows — carries GO:0031491 nucleosome binding IDA from
PMID:39676660 in its own record. That term has not reached ACTR5 or any other
ARP5 ortholog. Checked across the family with QuickGO: of ACTR5, fly, yeast,
pombe and Arabidopsis ARP5, plus human ACTR8, ACTL6A, ACTR6, ACTR1A and ACTR10,
only yeast ARP5 (GO:0031491, IDA), ACTL6A (GO:0031492, HDA;
GO:0003682) and ACTR6 (GO:0031491, IBA) hold anything in the
nucleosome/chromatin-binding branch, and not one of the eleven holds a
nucleotide-binding term.
So the missing MF is a family-level PAINT gap, not a human oversight — and it is
the same family-wide nucleotide-binding gap that the ACTR1A, ACTR1B and ACTR10
reviews independently reported for the dynactin ARPs. Filed as a single PAINT
recommendation in suggested_questions, naming the node once.
Three pieces of evidence bear on whether human ARP5 binds histones directly.
Reading (3) as refuting (1) would be the error the campaign made on ACTR10, where
a true verbatim quote was selectively bounded. The 2026 statement is about the
nucleosome acidic-patch-binding foot, which is a different surface from the
free-dimer-binding hydrophobic/acidic patch that the yeast work maps. So
GO:0042393 histone binding is proposed as a NEW annotation (IDA,
PMID:29643506), with the concentration/replication limitation and the missing
foot recorded in knowledge_gaps rather than suppressed.
GO:0005515 — fourteen rows, adjudicated per partnerAll five partner accessions resolve to reviewed Swiss-Prot canonical entries of
the expected length — no TrEMBL or ORFeome substitutions of the kind found on
ACRV1:
| accession | gene | length | reviewed | first GOA row |
|---|---|---|---|---|
| Q9H981 | ACTR8 (ARP8) | 624 | Swiss-Prot | PMID:16230350 |
| Q9ULG1 | INO80 | 1556 | Swiss-Prot | PMID:19014934 |
| Q16531 | DDB1 | 1140 | Swiss-Prot | PMID:20855601 |
| Q6PI98 | INO80C (IES6) | 192 | Swiss-Prot | PMID:26496610 |
| O60437 | PPL (periplakin) | 1756 | Swiss-Prot | PMID:32296183 |
Uniform rule applied, stated once so the verdicts are not ad hoc:
protein binding adds nothing thatpart_of GO:0031011 Ino80 complex does not already say, and whole-complextwo hybrid array + two hybrid prey
pooling approach + validated two hybrid — which is where UniProt'sNbExp=3 comes from. Exactly the ACRV1 pattern: one experiment counted threeIntAct check run in full (130 records): the only non-INO80, non-histone partners
are high-throughput singletons, including an E. coli argI two-hybrid hit
(PMID:20711500, a human–bacterial-pathogen interactome screen) which GOA has
correctly not imported.
Five IMP rows come from ComplexPortal annotating CPX-846 (the INO80 complex) and
projecting onto every subunit:
| term | reference | what the paper actually perturbed |
|---|---|---|
GO:0006275 reg. of DNA replication |
PMID:25016522 | INO80 and ARP8 |
GO:0060382 reg. of DNA strand elongation |
PMID:25016522 | INO80 and ARP8 |
GO:0033044 reg. of chromosome organization |
PMID:26340092 | INO80 / "INO80 complex" knockdown |
GO:0051726 regulation of cell cycle |
PMID:26340092 | as above |
GO:0045893 pos. reg. of DNA-templated transcription |
PMID:27641337 | INO80 and INO80B in NSCLC |
PMID:25016522's full text is cached and contains zero occurrences of "Arp5" or
"ACTR5" (grep -ci = 0); its knockdowns were
PMID:25016522
and
PMID:25016522.
PMID:26340092 and PMID:27641337 are abstract-only in the cache, so what their
full texts assayed cannot be checked from here.
These are not removed. Projecting a complex-level process onto an obligate
subunit is legitimate GO practice, and ACTR5 is required for the complex's
catalytic activity (§1). They are marked KEEP_AS_NON_CORE: the biology is
INO80's, one step removed from ARP5's own molecular function. The evidence-code
question — IMP on a gene product that was not itself perturbed — is raised once,
as a recommendation to ComplexPortal/GO, not repeated per row.
GOA gives ACTR5 GO:0045893 positive regulation of DNA-templated transcription
(IMP, from a paper about INO80/INO80B in lung cancer) and nothing negative. The
one study that assayed ACTR5 itself at a promoter found the opposite sign:
Hence a NEW GO:0000122 negative regulation of transcription by RNA polymerase II
(IMP), with the caveats stated in the row: HepG2/HCC-specific, single study, and
the study carries a 2025 erratum (PMID:41071901) correcting Fig. 2D — the
CDKN2A western — because the ACTR5 and U87 panels were inadvertently duplicated
from Fig. 3A. The publisher states the conclusions are unaffected, and the mRNA
(RNA-seq), ChIP-qPCR and H3K9me2 evidence is independent of the corrected panel.
The sign of ACTR5's transcriptional effect is therefore locus-dependent, and
neither the existing positive row nor the new negative row should be read as the
gene's general behaviour.
The paper's "INO80-independent" claim is not adopted. Its title asserts it,
but the support is the absence of a HepG2-selective essential domain in the
other subunits
PMID:36563143,
and the requirement it does map — the surface region A5 (G502–S519) — works
through IES6
PMID:36563143,
which is itself an INO80 subunit (INO80C). Differential CRISPR dependency can
reflect differential redundancy rather than complex-independence. Recorded in
knowledge_gaps, not as an annotation. Affinage's record rests almost entirely
on this paper and cites it without flagging the erratum.
Both are nuclear ARPs in human INO80, so the two reviews will overlap on the
complex and on the shared literature. They differ in three checkable ways:
HEDKS, losingDDSCH). Neither is an ATPase; onlyAlso note that the PMID:25016522 replication annotations projected onto ACTR5
(§9) rest on experiments in which ARP8 was the subunit knocked down — so for
ACTR8 the same rows have direct support that they lack for ACTR5.
39 review rows, one per GOA line. The GOA TSV has 40 data lines; the seeded
review collapses them to 34 on (term, evidence, reference, qualifier). The five
collapsed GO:0005515 rows are restored here so each interaction partner is
adjudicated separately (the two partners on PMID:20855601 receive different
verdicts). The one remaining exact duplicate — GO:0031011 IDA PMID:21303910
asserted by both ComplexPortal and UniProt, identical in every
schema-representable field — is reviewed once.
| action | n | rows |
|---|---|---|
| ACCEPT | 12 | chromatin remodeling ×2 (IBA, IDA), Ino80 complex ×3 (IBA, IDA ×2), nucleus ×4 (IEA, EXP, IDA ×2), UV-damage excision repair, DSB repair, nucleoplasm |
| KEEP_AS_NON_CORE | 10 | reg. of DNA-templated transcription (IBA), cytoplasm (IEA, IDA), 5 ComplexPortal projections, ACTR8 + DDB1 protein-binding rows |
| MODIFY | 1 | GO:0030234 → GO:0060590 + GO:0140658 |
| MARK_AS_OVER_ANNOTATED | 16 | is_active_in cytoplasm IBA, 3 ARBA parents, 12 redundant/noise GO:0005515 rows |
| NEW | 4 | GO:0031492, GO:0043531, GO:0042393, GO:0000122 |
Totals: 39 reviewed GOA rows + 4 NEW = 43. Counts are recomputed from the YAML
by ACTR5-bioinformatics/audit_review.py, which is the authority; the table
above is copied from its output.
Two committed scripts, both tested by deliberate mutation rather than by reading:
ACTR5-bioinformatics/nucleotide_site.py — four break-tests fire correctly:O15507 aborts because the returnedprimaryAccession is P56159, not what was asked for; and swapping ARP5'sours=HEDKS theirs=DDSCH). Re-running the pair of scripts reproducesresults.json and RESULTS.md byte-for-byte.ACTR5-bioinformatics/audit_review.py — six break-tests, all firing: deletingsource_entities token, emptying one IPI row'ssupporting_entities, injecting a forbidden claim, deleting a required claim,yaml.dump hard-wraps long scalars, so the phrase was split across a linejust validate-references) reportsTotal checks: 0 on a clean file, which reads like a no-op; corrupting one[ERROR] Title mismatch for PMID:29643506, so it isjust fetch-gene human ACTR5; just fetch-gene-pmids human ACTR5;just fetch-pmid for 26306040, 16618800, 39676660, 41775336, 36563143,self_evaluation_pairwise: win, trust gates clear, 2 citations, 3 findings. Both citedPMID:bio_* preprint ids). Neither isrelevance: LOW and supports no annotation.size=2,primaryAccession guard) and QuickGO annotation search withgoUsage=descendants&goUsageRelationships=is_a,part_of./ontology/go/terms/<ids>/complete (reading isObsolete and secondaryIds)/ancestors: GO:0060590 is a direct child of GO:0030234;GO:0031492 has GO:0031491, GO:0003677 and GO:0003682 among itsGO:0001671 is not under GO:0030234.source_entities on every propagation_review were generated from the GOAThe reviewer raised two blocking items and three suggestions. Verified before
conceding, per the campaign rule that the reviewer's checkable premises should be
checked:
GO:0001671 / GO:0060590. Partly conceded, partly pushedGO:0030234"GO:0001671 is confirmed by both QuickGO and OLS; the reviewer'sGO:0060590 is not what either reports. But theGO:0060590 is a grandchild, not a direct childGO:0060589 sits between), and right that listing two parents forGO:0001671 was redundant. Both corrected, and GO:0001671 is now offered assupporting_text entries that pass the verbatim check but do not supportis_active_inpart_of GO:0031011 row areoriginal_reference_id for theGO:0043531 IDA (ACTR1A precedent). Taken: now PMID:41775336, with thesupported_by and the note that 7ZI4 — thenucleotide_site.py now