This entry supersedes the biological judgments in the earlier journal entry where they conflict. The original entry is retained verbatim as historical provenance. The current review retains all 305 machine assertions and the single pre-existing author proposal for negative regulation of FGFR signaling. It does not create another annotation or reinterpret that historical proposal as a new machine assertion. The frozen project association remains autosomal dominant CBL-related disorder, classified Definitive in the frozen inventory; no disease-validity status is changed here.
CBL is a RING ubiquitin E3 ligase. It recruits an E2 and promotes ubiquitin transfer rather than acting as an E2 or forming the catalytic thioester intermediate characteristic of HECT E3s. The primary biochemical source establishes E2-dependent ligase activity (PMID:10514377). Human CBL structures and biochemical controls in PMID:22266821 distinguish an autoinhibited arrangement from Tyr371-phosphorylated CBL, including changes in E2 affinity and positioning. Selected original structural Results and Methods were read; those assays use purified fragments and peptides, not a complete native receptor signaling assembly.
The TKB module recognizes selected phosphotyrosine motifs. PMID:18273061 supplies positive peptide structures and binding comparisons for several partners, but its wild-type FLT1 peptide does not bind under the tested conditions; engineered substitutions restore binding. The FLT1 source row therefore remains uncertain rather than being forced into the positive group. The APS distinction also matters: Figure 5A directly measures APS phosphopeptide binding by calorimetry, including a pH-dependent comparison, while Figure 4G uses full-length CBL, rat myc-tagged APS and IR-B in a mutational binding assay. The independent CBL–APS phosphopeptide crystal structure and additional calorimetry are from PMID:15737992. The source row's partner identifier remains unchanged.
CBL's proline-rich sequences engage SH3 domains on partners such as CIN85, intersectin, SRC and ABI1. These are supported domain-binding refinements, not claims that CBL possesses those SH3 domains. Conversely, CRK/CRKL or PI3K p85 can recognize phosphorylated CBL through their own SH2 domains. That direction does not give CBL phosphotyrosine-reader activity on the CRK/p85 edge. The same distinction applies to 14-3-3 proteins recognizing serine-phosphorylated CBL. The three core functions summarize E3 chemistry, TKB phosphotyrosine recognition and binding to partner SH3 domains; they do not duplicate every downstream signaling outcome. Key sources include PMID:15090612, PMID:16914641, PMID:17094785, PMID:8524328, PMID:8626543, PMID:9160881 and PMID:9092538.
CBL ubiquitination supports receptor sorting and attenuation, with substrate- and cell-dependent alternatives. PMID:15465819 distinguishes routes by which CBL directs activated EGFR into Eps15-containing pits. Its experiments do not make every CBL-associated protein a ubiquitination substrate. Human CBL disease-associated substitutions tested in COS-7 cells impair EGFR ubiquitination, internalization and degradation and increase ERK signaling (PMID:25178484). This is construct evidence for the tested variants, not proof that every clinical CBL allele has the same quantitative effect. The Noonan-like/JMML context is also recorded in reviewed UniProt; the frozen clinical association is preserved separately from individual assay conclusions.
For FGFR, PMID:11997436 supports recruitment through FRS2alpha–GRB2 and receptor/adaptor ubiquitination, while PMID:21596750 provides human mesenchymal-cell perturbation evidence involving FGFR2 and PDGFRA. The FGFR3 disease-mutant study PMID:17509076 reports a context in which receptor ubiquitination appears CBL independent. That result limits universal substrate claims; it does not contradict CBL's established E3 activity. The genuine historical FGFR-downregulation proposal remains. The earlier SPRY/SULF comparison was not a same-role E3 comparison and is not used to manufacture further process coverage. The two exact target-containing cached GO-CAMs inspected here concern LAG3, not FGFR; they do not establish absence from every external model.
The source-specific PI3K direction is corrected in the human Saethre–Chotzen osteoblast study. CBL re-expression reverses elevated PI3K/Akt signaling, supporting negative regulation for that assertion (PMID:17003487). This does not exclude PI3K recruitment or activation in different CBL complexes. The Reactome PTK6 pathway's specific positive-EGFR assertion remains uncertain because its CBL-specific causal role was not resolved; CBL's usual inhibitory role alone is insufficient to reject a curated pathway context.
PMID:40101708 distinguishes nondegradative ubiquitination from receptor clearance. The available canonical cache is abstract-only. Selected primary Results, figure captions and Methods were read in the author-paper reproduction. Human Jurkat double-knockout/reconstitution and primary T-cell experiments support redundancy between CBL and CBLB. Single-gene loss does not recapitulate all double-loss effects. K63-specific antibody and ubiquitin-mutant controls support K63 chains; the abstract's broader non-K48 wording alone would not establish that linkage. The cell-derived substrate ubiquitination experiment is not represented as an entirely purified binary CBL–LAG3 assay. K11 and possible quality-control K48 observations are not generalized into new CBL chain-specific functions.
The study found no increased LAG3 half-life, but the current GO:0050821 definition includes structural integrity as well as protection from degradation or aggregation. The paper proposes a membrane-dissociated signaling-tail conformation. The two inspected cached LAG3 GO-CAMs explicitly model CBL-dependent ubiquitination within protein stabilization and T-cell signaling. Those positive curator models are a material counterweight to a simple half-life-based rejection. Whether the conformational mechanism meets the term's structural-integrity meaning remains unresolved; both stabilization rows remain UNDECIDED rather than being removed.
The new normal cache of PMID:16301331 contains XML text. Its complete relevant Results, Discussion and Methods were read; figure captions were read as text, without independently inspecting all image pixels or supplements. The rat experiments manipulate androgen availability with flutamide, hypophysectomy and testosterone replacement, and use Sertoli/germ-cell cultures. The mouse Cbl knockout adds a functional androgen-withdrawal/apoptosis phenotype. This supports a bounded non-core testosterone response; it is more than an expression observation. It does not show direct CBL binding to androgen or prove that Bim/Smac are direct CBL ubiquitination substrates. The paper's failed direct substrate tests and the imbalance between pro- and anti-apoptotic factors remain relevant limits.
The same study reports disorganized adult seminiferous architecture, germ-cell abnormalities and male hypofertility. The old assertion that the mice were simply fertile or lacked gonadal evidence is not retained. The exact male-gonad-development term concerns development of the mature structure, however, and the distinction between developmental establishment and adult maintenance is not settled by these results. The proposed early postnatal apoptosis explanation was not the demonstrated endpoint. That source row remains UNDECIDED with a concrete developmental-stage question.
The irradiation experiment has a different purpose. Local irradiation progressively removes testicular cell populations, allowing the authors to localize the source of CBL transcript/protein expression. The observed abundance changes do not demonstrate CBL executing a gamma-radiation response. The corresponding electronic transfer is marked over-annotated on this inspected experimental scope, not because IEP evidence is intrinsically invalid or because CBL could never respond to radiation.
The second new XML cache, PMID:19546888, contains actual perturbation evidence. In rat neuronal systems, CBL/CBLB knockdown sensitizes cells to NGF deprivation and DNA damage; loss of protein abundance is not the only observation. Human HEK293 experiments and construct controls also place c-Cbl upstream of MLK-to-MKK/JNK signaling. WT and RING-defective c-Cbl can protect against MLK-driven death in the tested context, and c-Cbl does not simply degrade MLK3 there. CBLB does not reproduce every c-Cbl overexpression phenotype. Endogenous POSH co-immunoprecipitation was unsuccessful, whereas other association assays were positive; a purified universal binary interaction is not asserted. The DNA-damage, NGF and negative-apoptosis transfers are retained as bounded non-core biology.
That protective setting does not erase the opposite causal direction in PMID:18070883. In the inspected human SW13 experiments, SPRY2 sequestration of CBL preserves growth-factor receptor signaling and survival; dominant-negative CBL rescues the receptor/survival effect of SPRY2 depletion. The specific negative-apoptosis annotation is over-annotated for that source. This is not a claim that CBL cannot suppress apoptosis elsewhere, as PMID:19546888 shows. Unread hypoxia, starvation, ethanol and other donor-specific mechanisms are left uncertain rather than being rejected using an expression-code shortcut.
All 122 generic binding rows were reviewed individually. Supported generic associations are kept as non-core under the project's explicit standing instruction; 41 are refined where evidence establishes the relevant binding activity, and two remain uncertain. The second uncertainty is the INPPL1 row carrying PMID:5668240: the actual cached publication concerns peracetic acid, but the intended citation has not been verified. No replacement PMID is invented. Exact partner identifiers, including xenolog and tested-product identifiers, remain unchanged. Curated UniProt edges can corroborate a qualitative association; they do not convert an unread original high-throughput target table into a verified primary assay or a direct binary interface.
PMID:21706016 is an affinity-purification/selected-reaction-monitoring study of GRB2 complexes in HEK293T cells. AP-SRM is a method name, not evidence of APS-driven recruitment. Its source-specific CBL table remains uninspected; independent CBL–GRB2 evidence supports retaining that qualitative edge. The corrected final rationale distinguishes those facts.
CBL is retained in cytosol and at the cytoplasmic side of plasma-membrane signaling complexes. Reactome source rows retain the original curated locations with independent CBL trafficking support; an event named for another enzyme does not confer that enzyme's activity on CBL. The complete 78 unique cached Reactome summaries were read, but the entire physical-entity hierarchy was not re-fetched. Golgi/ciliary observations in PMID:29237719 include human CBL constructs in mouse cells and endogenous mouse contexts; they are kept as contextual locations without pretending every image is endogenous human protein. Flotillin-complex membership and the exact CBL target in the E-cadherin proteomics source remain unresolved.
Every reference receives a manual assessment. All 80 canonical publication headers and complete available abstracts were read. A true full-text flag does not guarantee complete extraction: PMID:18070883 contains abstract/Discussion but lacks cached Results/Methods; PMID:18273061 likewise lacks the cached original Results/Methods used in the finer structural assessment; the richer external readings are identified separately. PMID:25468996 does not expose the decisive target table in its available cache. Original screen-table uncertainty remains explicitly UNVERIFIED where appropriate, even if an association is independently retained.
The PMID:11997436 correction changes an author's name, and PMID:17509076 has an authorship correction; neither was treated as an experimental retraction. The corrected Figures 2/3 associated with PMID:14661060 were not independently inspected, so their unresolved detail does not support a confident new interface claim. The historical Falcon report is preserved as orientation, not substituted for primary evidence. Newly authored short anchors in the YAML were verified against exact canonical bytes, with at most 25 aggregate words per publication; this appendix adds no repeated quotation. Earlier journal quotations remain untouched historical text.
The exact source inventory contains 30 14-3-3 partner rows across seven human family members, including the two SFN/P31947 rows. Four already used GO:0071889; the other 26 are now refined to that same term. The current GO definition specifies binding to the 14-3-3 protein class. It does not assert that CBL reads a phosphoserine residue or dictate which interface performs the association. Each exact partner is independently corroborated in the reviewed UniProt interaction record. The complete early abstracts support CBL–14-3-3 association, including the tau/zeta and stimulus-dependent controls [PMID:11157475; PMID:15094368; PMID:8663231; PMID:9092538; PMID:11697890]. The original pair-level records for several systematic studies remain uninspected; this narrower description does not turn them into newly verified direct-binding assays. The explicit project generic-binding override continues to govern supported associations for which a more informative activity is not established.
GRB2 requires a different distinction: GO:0017124 names contact with an SH3 domain, not simply contact with any part of an SH3-containing protein. Selected original publisher Results for PMID:17094785 now distinguish peptide 494 competition with GST-GRB2 from the SRC-preferring peptide 540; the former is reported as data not shown. Independent PMID:11997436 Results use GST N-/C-SH3 domains and GRB2 deletion constructs, including HEK293 cells, to establish the direction of CBL recruitment. These are cellular/lysate assays, not an all-purified thermodynamic reconstruction. Two original rows are refined: the motif experiment and the cooperative receptor-recruitment row PMID:23799367, with the latter's domain assignment explicitly supported by the separate mechanistic study. Ten network/coassociation rows remain qualified non-core: their original interfaces are unresolved and could involve another GRB2 contact or a larger complex. The phosphorylation-dependent PMID:25814554 context particularly does not warrant automatic SH3 attribution. The unresolved domain mapping is now an explicit biological question. PMID:19380743 is correctly identified as BCR-ABL AP-MS in K562 cells; it is distinct from the later kinase-assisted two-hybrid study. All exact source partners and evidence codes remain unchanged.
The E3 core now encodes GO:0070534 protein K63-linked ubiquitination in place of the generic ancestor GO:0016567, while its description retains broader substrate-dependent ubiquitination. The already inspected external primary Results of PMID:40101708 include linkage-selective ubiquitin mutants and linkage-specific antibodies, in addition to CBL/CBLB double-loss and individual rescue in human T-cell systems. The K63 call does not follow merely from the abstract's non-K48 wording. CBL and CBLB redundancy, cell-derived LAG3 in the reconstitution, and the unvalidated K11 linkage remain explicit limits. No new BP annotation or duplicate E3 core is added.
The same E3 core now includes membrane raft, supported by the human osteoblast biochemical/immunocytochemical context in PMID:18374639. Its short cached anchor is “FGFR2 and Cbl interact in raft micro-domains” (the cached line break is preserved in YAML). The study connects FGFR2 recruitment, CBL Y731-dependent PI3K association, PI3K ubiquitination/degradation and raft microdomains. The full paper remains unavailable in the canonical cache; no universal raft localization or new microscopy claim is added. Plasma-membrane and cytosolic contexts remain relevant for other E3 substrates. The location follows this target-specific evidence, not the machine qualifier alone.
The optional PTK6 question is partly resolved from the existing complete human Reactome records [Reactome:R-HSA-8849469; Reactome:R-HSA-8848818; Reactome:R-HSA-8848829]. The specific autoubiquitination event explicitly assigns CBL an executed ubiquitin-transfer step before its degradation. The existing TAS positive-EGFR process is therefore retained as non-core in that defined route; CBL is not treated solely as a passive inhibited target. The source primary full text was not inspected; this remains deference to the explicit curated reaction, with no change to the well-supported general negative receptor-regulatory role.
This focused revision preserves all 305 machine assertions and the one genuine historical NEW record, all 166 reference identities/titles, source flags, current source bytes, previous histories and research artifacts. No NEW assertion is created. The new membrane-raft snippet occurs once in YAML and once in this appendix; combined with pre-existing uses, the per-source word audit remains bounded. The earlier journal above is preserved verbatim as historical provenance. The biological description is shortened by removing two explanatory contrasts. Temporary source-recovery and consultation records support this work but are not represented as canonical primary caches.