PF11289: bCoV_viroporin

Betacoronavirus viroporin

Curation status: SEEDED
Seed status: EX DUF
Characterization: UNSCORED

Grounding

PF11289: Betacoronavirus viroporin
IPR024407: integrated entry for Betacoronavirus viroporin

Source description

This entry represents protein 3a encoded by Orf3/3a, also known as X1, which forms homotetrameric potassium, sodium or calcium sensitive ion channels (viroporin) that causes ER-stress in host cells and may modulate virus release. This is a pro-apoptosis-inducing protein that localises to the endoplasmic reticulum (ER)-Golgi compartment. SARS-CoV causes apoptosis of infected cells through NLRP3 inflammasome activation [InterPro reference PUB00075660,InterPro reference PUB00075661,InterPro reference PUB00056032,InterPro reference PUB00075662]. Protein 3a also promotes the ubiquitination of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) mediated by its interaction with TNF receptor-associated factor 3 (TRAF3). This protein induces NF-kappa B activation and upregulates fibrinogen secretion with high cytokine production [InterPro reference PUB00094124]. Through the activation of the PERK pathway of unfolded protein response (UPR), this protein causes phosphorylation of eIF2-alpha leading to reduced translation of cellular proteins and as the activation of pro-apoptotic downstream effectors (i.e ATF4, CHOP).

Evidence and references

InterPro entry and its literature references. PUB identifiers are internal InterPro references, not PubMed identifiers. Unresolved citations link to the originating entry.
Frozen description source: InterPro/Pfam API

Source descriptions and links are provenance, not independent functional validation.

Evidence counts: not scored.

Curated functional assertions

No curated functional assertions supplied.

Protein sequence examples

3 verified sequence examples. FASTA

UniProt	Protein / organism	Sequence	Provenance
P0DTC3	ORF3a protein Severe acute respiratory syndrome coronavirus 2	275 aa; version 1 UniProt 2026_03	UNIPROT FETCH 1 sibling references ProteinTraitsMech: Pfam:PF11289
P59632	ORF3a protein Severe acute respiratory syndrome coronavirus	274 aa; version 1 UniProt 2026_03	UNIPROT FETCH 1 sibling references ProteinTraitsMech: Pfam:PF11289
Q3LZX0	Protein 3 Bat coronavirus HKU3	274 aa; version 1 UniProt 2026_03	UNIPROT FETCH 1 sibling references ProteinTraitsMech: Pfam:PF11289

Pfam membership is not functional evidence. Whole-protein sequences do not establish domain boundaries. A coverage gap here is not absence from UniProt.

Sequences and metadata: UniProt Consortium, CC BY 4.0.

Domain matches

No residue-level domain match evidence is available in this build. Structure and AlphaFold counters do not supply coordinates or establish function.

Snapshot counters

proteins: 78
matches: 78
proteomes: 3
taxa: 58
structures: 6
alphafold models: 2
domain architectures: 1

Classification basis

pfam previous unknown name

No scoring reasons supplied.

Related Mech records

This family joined the worklist after the frozen cross-Mech scan, so other Mechs were not searched for it. Missing links here are not evidence that other Mechs lack it; rows shown come from mentions of a former DUF/UPF name.

No cross-Mech examples are present in the supplied snapshot.

Curation history and reviews

No retained curation events supplied.

No retained review supplied.

Record source

data/families/PF11289.yaml
Family YAML in this build

Download this family (JSON)

Status and evidence

Seed status: A name-based classification of frozen InterPro/Pfam metadata. UNKNOWN CANDIDATE means the metadata explicitly says the function is unknown. KNOWN HISTORICAL DUF means a DUF name matched without that wording; this heuristic is not proof of a known function and does not establish experimental characterization. EX DUF means Pfam renamed the family away from a DUF/UPF name, as recorded in Pfam's previous identifiers; a rename usually follows published work on some members but is naming history, not proof of function for every member. Some EX DUF families' current names or descriptions still say the function is unknown; their classification basis lists this, and scoring does not treat them as characterized. FALSE POSITIVE TEXT HIT means the naming rules did not match.
Characterization: A separate evidence-scoring result. UNSCORED means no score has been calculated; it is not evidence that the family lacks a known function. Missing scores are not negative evidence. PARTIALLY CHARACTERIZED has partial support; KNOWN HISTORICAL DUF can inherit the seed label or reflect a known-function signal. Neither label implies experimental validation.
Evidence counts: Source-specific signals, not unique proteins, publications, or confidence scores. Known counts Rhea reactions and experimentally supported GO molecular-function annotations. Partial counts functional/domain assignments. Context counts structural, environmental, orthology, interaction and neighborhood signals; context alone does not assign function. Repeated annotations may not be independent.
Curation status: Reported separately from seed classification and characterization. SNAPSHOT ONLY means no curated metadata was supplied for this build. SEEDED denotes a source-derived record, not an expert-reviewed functional claim.
Missing counts: Not available means the source did not supply that counter. A zero is a reported count. Not scored means evidence counts are unavailable.