id: F7J0N2
gene_symbol: RGA5
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:39947
  label: Oryza sativa Japonica Group
description: >-
  RGA5 (Os11gRGA5, SasRGA5) is a 1,116-residue intracellular coiled-coil
  nucleotide-binding leucine-rich repeat (CC-NB-LRR, NLR) immune receptor
  encoded at the Pia/Pi-CO39 blast-resistance locus on rice chromosome 11,
  where it lies head-to-head with its partner NLR gene RGA4. RGA5 is the
  sensor of the pair. Its C-terminal region, after the LRR, carries an
  integrated heavy-metal-associated (HMA; also called RATX1) domain that
  directly binds the sequence-unrelated MAX-family effectors AVR-Pia and
  AVR1-CO39 secreted by the rice blast fungus Magnaporthe oryzae. The HMA
  domain has a canonical HMA fold, but its metal-binding motif is degenerate,
  so it acts as an effector-binding decoy rather than as a metal-binding
  module. In the absence of effector, RGA5 forms homo- and hetero-complexes
  with RGA4 through their coiled-coil domains and represses the autoactive,
  cell death-inducing activity of RGA4; the RGA5 CC domain is required for
  this repression while the HMA domain is dispensable for it. Effector binding
  to the HMA domain relieves the repression, so that RGA4 triggers a
  hypersensitive cell death response and resistance. RGA5 does not itself
  activate cell death, and an intact RGA5 P-loop is not needed for repression
  or for effector recognition. Only the RGA5-A splice form, which keeps an
  intact HMA domain, is functional; the intron-retaining RGA5-B form is
  inactive. Both RGA5 and RGA4 localize mainly to the cytosol and do not move
  to the nucleus on effector recognition. RGA5 has become a scaffold for
  engineering new recognition specificities by redesigning its HMA domain.
alternative_products:
- name: 1 (RGA5-A)
  id: F7J0N2-1
- name: 2 (RGA5-B)
  id: F7J0N2-2
  sequence_note: VSP_059636, VSP_059637
alternative_records:
- id: Q2R8L1
  relationship: REFERENCE_PROTEOME_CANDIDATE
  reference_proteome: UP000059680
  reviewed_on: '2026-10-19'
  reason: Retain F7J0N2 as the primary Swiss-Prot accession. Q2R8L1 is a plausible reference-proteome
    counterpart, but the captured evidence does not independently map the Sasanishiki protein to the Nipponbare
    locus. The target is named RGA5 at Os11g0225300 / LOC_Os11g11810; those identifiers locate the target
    only. The sequence is substantially divergent (624 identities over 1105 paired residues, with 207
    gap columns), and the cultivar-dependent AVR-Pia recognition statement concerns the resistance system.
    Retain a candidate pending cross-cultivar locus mapping; do not assert equivalent receptor specificity
    or protein integrity.
  evidence:
  - type: PROTEOME_SEARCH
    description: MMseqs2 searched 48,896 sequences across UP000059680 at E <= 1e-5 and sensitivity 7.5,
      returning 404 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10
      and extension -0.5. Scores and sequences for all 404 returned candidates are retained, with 10 detailed
      alignment files. The heuristic search does not establish genomic absence or unique locus identity.
    supported_by:
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'target_sequence_count: 48896'
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'candidate_count: 404'
  - type: SEQUENCE_COMPARISON
    description: 'Q2R8L1: 624 identities across 1312 global-alignment columns (47.561% identity including
      gaps), 481 substitutions and 207 gap columns. Query coverage is 99.0143%; target coverage is 84.9347%.
      Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 56.4706%
      (624/1105); gap columns are excluded from this denominator.'
    supported_by:
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: |-
        query_length: 1116
          target_length: 1301
          alignment_columns: 1312
          identities: 624
          mismatches: 481
          gap_columns: 207
          identity_percent: 47.561
          query_coverage_percent: 99.0143
          target_coverage_percent: 84.9347
  - type: PROTEOME_MEMBERSHIP
    description: The primary accession is outside every searched exact-taxon reference proteome. Current
      UniProt records place Q2R8L1 in UP000059680 and give it the same taxon as the primary.
    supported_by:
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'primary_in_any_reference_proteome: false'
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'alternative_in_reference_proteome: true'
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'same_taxon: true'
  - type: RECORD_HISTORY
    description: 'Sampled UniSave observations: 09-DEC-2015, entry version 12.: no Proteomes cross-reference;
      11-DEC-2019, entry version 31.: no Proteomes cross-reference; 27-NOV-2024, entry version 45.: no
      Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence,
      the exact change date, or UniProt''s motivation.'
    supported_by:
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: |-
        entry_date: 09-DEC-2015, entry version 12.
          proteomes: []
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: |-
        entry_date: 11-DEC-2019, entry version 31.
          proteomes: []
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: |-
        entry_date: 27-NOV-2024, entry version 45.
          proteomes: []
  - type: CURATION_CONTEXT
    description: The target record names the Nipponbare locus Os11g0225300 / LOC_Os11g11810. These target-only
      identifiers and the cultivar-dependent AVR-Pia recognition statement do not independently establish
      correspondence to the Sasanishiki locus.
    supported_by:
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: cultivars Nipponbare, Mokoto and Hitomebore
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'value: Os11g0225300'
    - reference_id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
      supporting_text: 'value: LOC_Os11g11810'
existing_annotations:
- term:
    id: GO:0002758
    label: innate immune response-activating signaling pathway
  evidence_type: IDA
  original_reference_id: PMID:23548743
  qualifier: involved_in
  review:
    summary: >-
      RGA5 directly binds the M. oryzae effectors AVR-Pia and AVR1-CO39 and,
      together with RGA4, initiates the effector-triggered immune signaling that
      leads to resistance. As the receptor that perceives the ligand, RGA5 takes
      part in this signaling pathway.
    action: ACCEPT
    reason: >-
      RGA5 is the effector-binding receptor that starts the signaling pathway,
      so it does part of the work of the pathway rather than only being
      required for it. Direct binding is linked to function because an inactive
      AVR-Pia allele that does not bind RGA5-A is not recognized. GO:0002758 is
      the term used for plant NLR immune signaling (e.g. Arabidopsis RPS4).
      The more specific GO:0035872 (NLR receptor signaling pathway) is not used
      for any plant gene product, so it is not proposed here.
    supported_by:
    - reference_id: PMID:23548743
      supporting_text: revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A,
        providing evidence for the recognition of multiple Avr proteins by direct
        binding to a single R protein
    - reference_id: PMID:23548743
      supporting_text: Direct binding seems to be required for resistance as an
        inactive AVR-Pia allele did not bind RGA5-A
- term:
    id: GO:0002758
    label: innate immune response-activating signaling pathway
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00034398
  review:
    summary: >-
      ARBA machine-learning transfer of innate immune signaling to an NLR
      protein. The experimental IDA row for the same term supports it.
    action: ACCEPT
    reason: >-
      Consistent with experimental evidence that RGA5 is the effector receptor
      that starts RGA4-dependent immune signaling.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: RGA4 mediates cell death activation, while RGA5 acts as a
        repressor of RGA4 and as an AVR receptor
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25024433
  qualifier: enables
  supporting_entities:
  - UniProtKB:F7J0M4
  review:
    summary: >-
      IPI with RGA4 (F7J0M4). RGA5 and RGA4 form hetero-complexes through their
      coiled-coil domains, and RGA5 uses this association to repress the
      autoactive cell-death activity of RGA4. The repression is specific: RGA5
      does not suppress the autoactive NLRs Orin1 or L6.
    action: MODIFY
    reason: >-
      Protein binding is uninformative. The same paper shows what the binding
      does: RGA5 physically associates with RGA4 through the CC domain, and the
      CC domain is required for inhibiting RGA4-triggered cell death. This fits
      molecular function inhibitor activity (GO:0140678), which is defined as
      inhibition of a target's activity through non-covalent binding. This MF is
      what tells the sensor (RGA5) apart from the executor (RGA4).
    proposed_replacement_terms:
    - id: GO:0140678
      label: molecular function inhibitor activity
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: RGA4 and RGA5 form homo- and hetero-complexes and interact
        through their coiled-coil domains
    - reference_id: PMID:25024433
      supporting_text: Neither Orin1- nor L6 MHV -mediated cell death was suppressed
        by RGA5 showing that its inhibition activity is specific
    - reference_id: PMID:25024433
      supporting_text: The RGA5 CC domain is necessary but not sufficient for repression
        of RGA4-mediated cell death, while its RATX1 domain is dispensable
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:25024433
  qualifier: located_in
  review:
    summary: >-
      Functional Venus:RGA5 fusions co-localize with a cytosolic marker in rice
      protoplasts and are excluded from nuclei.
    action: ACCEPT
    reason: >-
      Directly supported by confocal imaging of a functional fusion protein.
      Cytosol (GO:0005829) is the more specific term, but cytoplasm is correct.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: Similar results were obtained for Venus:RGA5 which co-localized
        with Cerulean in the cytosol but not with NLS:Cerulean in the nuclei
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0086
  review:
    summary: UniProt subcellular-location mapping of the experimentally determined
      cytoplasmic localization.
    action: ACCEPT
    reason: Consistent with the IDA evidence from rice protoplasts.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: Localization studies in rice protoplast suggest that RGA4 and
        RGA5 localize to the cytosol
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: EXP
  original_reference_id: PMID:25024433
  qualifier: located_in
  review:
    summary: >-
      RGA5 is mainly cytosolic in rice protoplasts and does not move to the
      nucleus after AVR-Pia recognition.
    action: ACCEPT
    reason: >-
      The most specific location term with direct experimental support. It is
      where RGA5 binds effectors and associates with RGA4.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: Upon recognition of AVR-Pia, neither RGA4 nor RGA5 is re-localized
        to the nucleus
- term:
    id: GO:0006952
    label: defense response
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: >-
      InterPro2GO mapping from the plant disease resistance protein family
      (IPR044974). Broad but correct.
    action: ACCEPT
    reason: >-
      RGA5 is a resistance protein needed for effector-triggered defense against
      M. oryzae. The term is general but not wrong.
    supported_by:
    - reference_id: PMID:21251109
      supporting_text: SasRGA4 and SasRGA5, that are located next to each other and
        oriented in the opposite direction are necessary for Pia function
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00091908
  review:
    summary: >-
      ARBA transfer of the hypersensitive response to an NLR. For RGA5 the
      hypersensitive cell death depends on its effector recognition, but RGA4
      carries it out.
    action: KEEP_AS_NON_CORE
    reason: >-
      RGA5 does not trigger cell death itself. Autoactive MHD-motif mutants of
      RGA5 cause no cell death, and the authors conclude that cell death
      signaling is activated only by RGA4. RGA5 sits upstream of the response
      as its receptor and gatekeeper, so the term is correct as an
      involvement but is not a core RGA5 function. It is core for RGA4.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: These results support the conclusion that cell death signaling
        is activated exclusively by RGA4 and that AVR-Pia binding does not lead to
        RGA5 activation but solely to RGA4 de-repression.
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IMP
  original_reference_id: PMID:23548743
  qualifier: involved_in
  review:
    summary: >-
      Genetic analysis shows that RGA5-A, but not RGA5-B, is needed with RGA4
      for AVR-dependent resistance. Hypersensitive cell death in response to
      AVR-Pia/AVR1-CO39 needs a functional RGA5.
    action: KEEP_AS_NON_CORE
    reason: >-
      The mutant evidence shows that RGA5 is necessary for the effector-induced
      hypersensitive response, which is consistent with its role as the
      receptor. RGA4 is the protein that actually executes cell death, so for
      RGA5 this is a downstream outcome rather than a core activity. The
      annotation is kept as non-core and is not removed.
    supported_by:
    - reference_id: PMID:23548743
      supporting_text: Genetic analysis showed that only RGA5-A confers resistance,
        while RGA5-B is inactive.
    - reference_id: PMID:25024433
      supporting_text: RGA4 triggers an AVR-independent cell death that is repressed
        in the presence of RGA5 in both rice protoplasts and Nicotiana benthamiana
- term:
    id: GO:0009626
    label: plant-type hypersensitive response
  evidence_type: IMP
  original_reference_id: PMID:25024433
  qualifier: involved_in
  review:
    summary: >-
      In rice protoplasts and N. benthamiana, RGA4 + RGA5 + AVR-Pia gives rapid
      cell death, and removing RGA5 or the effector changes the outcome. RGA5
      gates the hypersensitive response but does not execute it.
    action: KEEP_AS_NON_CORE
    reason: >-
      Same reasoning as the other hypersensitive response rows. The core RGA5
      contribution is captured by innate immune receptor activity, by
      inhibition of RGA4 activity, and by regulation of the plant-type
      hypersensitive response (GO:0010363, proposed below as the replacement
      for the PRR-signaling regulation term).
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: Upon recognition of the pathogen effector AVR-Pia by direct
        binding to RGA5, repression is relieved and cell death occurs.
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IDA
  original_reference_id: PMID:23548743
  qualifier: involved_in
  review:
    summary: >-
      Native RGA5 recognizes effectors of the fungus M. oryzae. Resistance to
      the bacterium Xanthomonas oryzae involving RGA4/RGA5 has been shown only
      in an engineered system. There, transgenic Xanthomonas strains carrying a
      designer TAL effector switched on an inducible copy of the fungal
      AVR1-CO39 gene in transgenic rice (PMID:27289079). The cited 2013 paper
      is cached as abstract only, and its abstract describes only fungal
      effector recognition.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      I am not disputing what the curator saw in the full text. The objection
      is biological. RGA5 does not perceive any bacterial molecule. Bacterial
      resistance needs a fungal effector to be expressed artificially, so it
      shows that the RGA4/RGA5 output can work against other pathogens. It is
      not a natural defense response of RGA5 to bacteria.
    additional_reference_ids:
    - PMID:27289079
    supported_by:
    - reference_id: PMID:27289079
      supporting_text: transgenic rice lines harboring the AVR1-CO39 effector gene
        from the rice blast fungus Magnaporthe oryzae, under the control of an inducible
        promoter, were challenged with transgenic Xoo and Xoc strains carrying a TAL
        effector designed to transactivate the inducible promoter
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  supporting_entities:
  - ARBA:ARBA00028625
  review:
    summary: >-
      ARBA machine-learning transfer of a defense response to bacterium term,
      common among NLRs. RGA5 recognizes only fungal effectors.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      No native bacterial recognition by RGA5 is known. Its only reported
      anti-bacterial activity depends on artificial expression of a fungal
      effector (PMID:27289079).
    supported_by:
    - reference_id: PMID:27289079
      supporting_text: This induced AVR1-CO39 expression and triggered BB and BLS
        resistance when the corresponding Pi-CO39 resistance locus was present.
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR002182
  review:
    summary: >-
      InterPro2GO mapping from the NB-ARC domain. RGA5 has an NB-ARC domain
      (residues 182-466), but no nucleotide binding has been measured for it.
      Its P-loop lysine (K210) is not needed for RGA4 repression or for
      effector-triggered derepression.
    action: KEEP_AS_NON_CORE
    reason: >-
      ADP binding is plausible from the domain, as NB-ARC domains of resting
      NLRs bind ADP. However, the K210R P-loop mutant of RGA5 keeps full
      function, so nucleotide binding is not part of the activity that makes
      RGA5 a sensor. This differs from RGA4, whose P-loop is essential.
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: However, an intact RGA5 P-loop motif is not necessary for repression
        of RGA4-induced cell death or for removal of this repression after AVR-Pia
        recognition.
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR006121
  review:
    summary: >-
      InterPro2GO mapping from the HMA domain (IPR006121). The RGA5 integrated
      HMA domain has the HMA fold, but the crystal structure shows that its
      metal-binding motif is degenerate: the second cysteine is replaced by
      serine. The domain works as an effector-binding decoy.
    action: REMOVE
    reason: >-
      The domain-to-GO mapping assumes the canonical MxCxxC metal-binding
      motif, which RGA5 lacks. No metal binding has been shown, and the HMA
      domain's function is binding the AVR-Pia and AVR1-CO39 effectors.
    supported_by:
    - reference_id: PMID:30355769
      supporting_text: The metal-binding motif, characteristic of HMAs, is degenerated
        in RGA5HMA, as only the first Cys is conserved, while the second is replaced
        by a Ser.
    - reference_id: file:ORYSJ/RGA5/RGA5-deep-research-falcon.md
      supporting_text: The RGA5 HMA fold resembles other HMA domains, but its characteristic
        metal-binding motif is
- term:
    id: GO:0062207
    label: regulation of pattern recognition receptor signaling pathway
  evidence_type: EXP
  original_reference_id: PMID:25024433
  qualifier: involved_in
  review:
    summary: >-
      RGA5 represses RGA4-mediated cell death without effector, and effector
      binding relieves this repression. RGA5 therefore regulates the
      RGA4-dependent immune response, which is well supported.
    action: MODIFY
    reason: >-
      The regulatory role is real, but the term is placed oddly. GO counts NLR
      signaling as a child of pattern recognition receptor signaling (GO:0035872
      is_a GO:0002221). In plants, however, "pattern recognition receptor"
      means cell-surface PAMP receptors, which are distinct from intracellular
      NLRs. The output that RGA5 is shown to control is RGA4-triggered
      hypersensitive cell death. The plant-specific term regulation of
      plant-type hypersensitive response (GO:0010363) fits better and covers
      both the repression and the effector-triggered release. "Negative
      regulation" was not chosen, because RGA5 is also what allows the
      response once it binds effector.
    proposed_replacement_terms:
    - id: GO:0010363
      label: regulation of plant-type hypersensitive response
    supported_by:
    - reference_id: PMID:25024433
      supporting_text: RGA5 can be regarded as an AVR receptor since it physically
        binds AVR1-CO39 and AVR-Pia (Cesari et al , 2013 ) and transduces AVR signal
        perception into a relief of RGA4 repression, resulting in resistance induction
        and HR.
- term:
    id: GO:0140376
    label: innate immune receptor activity
  evidence_type: EXP
  original_reference_id: PMID:28087830
  qualifier: enables
  review:
    summary: >-
      RGA5 directly binds AVR-Pia through its integrated RATX1/HMA domain, and
      this binding is needed for recognition and resistance. The same domain
      binds AVR1-CO39 (Kd about 5-7 uM; crystal structure, PMID:30355769). RGA5
      is the receptor of the RGA4/RGA5 pair.
    action: ACCEPT
    reason: >-
      This is the core molecular function of RGA5. The ligand is a pathogen
      effector perceived directly, and binding is coupled to triggering the
      immune response through derepression of RGA4. This MF should be on the
      sensor RGA5 and not on the executor RGA4, which does not bind the
      effectors.
    additional_reference_ids:
    - PMID:30355769
    supported_by:
    - reference_id: PMID:28087830
      supporting_text: The Magnaporthe oryzae effector AVR-Pia interacts with the
        decoy domain of the rice NLR immune receptor RGA5 through a defined surface
        area, and this interaction is required for effector recognition.
    - reference_id: PMID:30355769
      supporting_text: Mutations in the HMA-binding interface of AVR1-CO39 perturb
        RGA5HMA-binding, in vitro and in vivo, and affect the recognition of M. oryzae
        in a rice cultivar containing Pi-CO39
core_functions:
- description: >-
    Intracellular sensor NLR. It directly binds the M. oryzae MAX effectors
    AVR-Pia and AVR1-CO39 through its integrated C-terminal HMA (RATX1) decoy
    domain in the cytosol. This binding is the recognition event that starts
    effector-triggered immunity through its partner RGA4.
  molecular_function:
    id: GO:0140376
    label: innate immune receptor activity
  directly_involved_in:
  - id: GO:0002758
    label: innate immune response-activating signaling pathway
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:28087830
    supporting_text: The Magnaporthe oryzae effector AVR-Pia interacts with the decoy
      domain of the rice NLR immune receptor RGA5 through a defined surface area,
      and this interaction is required for effector recognition.
  - reference_id: PMID:23548743
    supporting_text: revealed direct binding of AVR-Pia and AVR1-CO39 to RGA5-A
- description: >-
    Inhibitor of its executor partner RGA4. Without effector, RGA5 forms a
    CC-domain-mediated hetero-complex with RGA4 and specifically holds back the
    constitutive cell death activity of RGA4. Effector binding relieves this
    inhibition without RGA5 itself becoming a cell death activator, so RGA5
    regulates the hypersensitive response rather than executing it.
  molecular_function:
    id: GO:0140678
    label: molecular function inhibitor activity
  directly_involved_in:
  - id: GO:0010363
    label: regulation of plant-type hypersensitive response
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:25024433
    supporting_text: RGA4 mediates cell death activation, while RGA5 acts as a repressor
      of RGA4 and as an AVR receptor
  - reference_id: PMID:25024433
    supporting_text: The RGA5 CC domain is necessary but not sufficient for repression
      of RGA4-mediated cell death, while its RATX1 domain is dispensable
suggested_questions:
- question: >-
    Sensor and executor NLRs in pairs such as RGA5/RGA4 (and RRS1/RPS4) get
    nearly identical electronic annotations: hypersensitive response, defense
    response, ADP binding. Should GO practice routinely give innate immune
    receptor activity and molecular function inhibitor activity to the sensor,
    and keep cell death execution terms for the executor?
- question: >-
    GO:0035872 (NLR signaling pathway) has no plant annotations, and plant NLR
    signaling is annotated as GO:0002758. Is this a deliberate convention, or
    should plant NLR pairs move to the NLR-specific term?
- question: >-
    Would a more specific MF child of innate immune receptor activity for
    direct pathogen-effector binding (as opposed to PAMP binding) be useful for
    sensor NLRs with integrated decoy domains?
suggested_experiments:
- description: >-
    Cryo-EM structure of the full-length RGA4/RGA5 hetero-complex with and
    without AVR-Pia, to find out how effector binding to the HMA domain
    relieves RGA4 repression without the complex dissociating.
- description: >-
    Metal-binding assays (ICP-MS, ITC with Cu/Zn) on the RGA5 HMA domain, and
    on a variant with the second cysteine restored, to test directly whether
    the degenerate motif has lost metal binding.
references:
- id: file:ORYSJ/RGA5/RGA5-record-evidence.yaml
  title: Compact archived record and sequence evidence for F7J0N2
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: PMID:21251109
  title: A multifaceted genomics approach allows the isolation of the rice Pia-blast
    resistance gene consisting of two adjacent NBS-LRR protein genes.
  findings: []
- id: PMID:23548743
  title: The rice resistance protein pair RGA4/RGA5 recognizes the Magnaporthe oryzae
    effectors AVR-Pia and AVR1-CO39 by direct binding.
  findings: []
- id: PMID:25024433
  title: The NB-LRR proteins RGA4 and RGA5 interact functionally and physically to
    confer disease resistance.
  findings: []
- id: PMID:27289079
  title: Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance
    to bacterial blight and bacterial leaf streak diseases.
  findings: []
- id: PMID:28087830
  title: Recognition of the Magnaporthe oryzae Effector AVR-Pia by the Decoy Domain
    of the Rice NLR Immune Receptor RGA5.
  findings: []
- id: PMID:30355769
  title: Specific recognition of two MAX effectors by integrated HMA domains in plant
    immune receptors involves distinct binding surfaces.
  findings: []
- id: file:ORYSJ/RGA5/RGA5-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report for RGA5
  findings: []
