FANCL provides the RING E3 and cognate E2-recognition activities of nuclear Fanconi anemia repair machinery. This guide combines the accepted target-study and database assessments while preserving their actual reading boundaries. The curation journal retains the earlier scoped assessments and their subsequent integration.
The human E3 function is supported by the original PHF9/FANCL discovery experiments (PMID:12973351) and purified human FANCL/UBE2T-dependent FANCI ubiquitination (PMID:19589784). The original human FANCL RING–UBE2T structure/binding experiments (PMID:24389026) establish E2 recruitment; the same paper's functional ubiquitination arm uses Xenopus FANCL/FANCD2. Human core membership is directly supported by PMID:20347428 and PMID:22343915. Chicken DT40 mutant/chromatin experiments (PMID:17938197) and Xenopus egg-extract repair experiments (PMID:19965384) remain conserved support, without being relabelled human.
PMID:16916645 and PMID:19111657 have verified positive abstracts but inaccessible operative original mains in the retained finite requests. Independently read human sources support the core functions and the UBE2T interaction. The UBE2W context from PMID:19111657 remains UNDECIDED. The historical combined UBE2W/UBE2T annotation now has separate partner-specific decisions. PMID:19111657 remains the unchanged original source; older acquisition prose that named PMID:22343915 for this expansion was a narrative typo.
PMID:22343915 contains positive human FANCL core-complex co-IP, but its inspected chromatin panel assays other core proteins. The specific human FANCL chromatin IDA context remains UNDECIDED. This is a limit of verified target-level evidence, not an assertion of curator error or negative localization.
The 2014 HI-II-14 study (PMID:25416956(https://pubmed.ncbi.nlm.nih.gov/25416956/)) used two proteome-scale yeast two-hybrid screens, fresh-colony retesting in quadruplicate and sequence confirmation. The 2020 HuRI/HI-III-20 study (PMID:32296183(https://pubmed.ncbi.nlm.nih.gov/32296183/)) used nine screens across three configurations, pairwise retesting and sequence confirmation. Original screening Methods, author-release FANCL pair records and PMID-specific IntAct validated-pair records support the 12 and 32 retained current partner contexts, respectively. Each row identifies its exact current partner and whether the author-release accession join is resolved. Seven historical joins remain unresolved; their current target identities rely on the PMID-specific IntAct records, without an invented historical mapping.
All 44 rows retain positive generic binding as non-core under the project's standing binding exception. These experiments test human-protein constructs in yeast. Network-level orthogonal validation does not establish that every FANCL edge received an orthogonal assay. The evidence alone does not establish physiological co-complex membership, FANCL substrate status or partner-derived enzymatic/signaling activity. Matching a base accession does not establish current isoform identity, and screen constructs do not prove equivalence of both natural FANCL products. ID2/Q02363 in HuRI is the transcriptional inhibitor, distinct from the FANCI–FANCD2 repair complex.
PMID:35512704 supports contextual association with SMAD4. Actual Data S1 Figure ivA page4 pixels show a weaker WT-SMAD4 pulldown band and a stronger G386D band for FANCL. Table S3B row23 records positive mutant-pair GST-pulldown and NanoPCA, with endogenous co-IP N/A. GO:0070410 co-SMAD binding is a specific refinement; no constitutive endogenous, substrate-ubiquitination or TGF-beta-process claim follows. An invalid reused supplement8.xlsx is retained as a failure, never interpreted as a valid table.
The inherited ubiquitin-binding proposal remains ISS. PMID:26149689 directly assays Drosophila ELF binding, Xenopus FANCL/N72R and chicken TAP-FANCL/ELF mutants. Human binding was not measured. ELF ubiquitin recognition is distinct from RING E2 recruitment and chemistry. No new process annotation is proposed, and both old quotations remain unchanged.
The following assessment was performed independently. A statement that a particular original was inaccessible here describes this database read, not the broader direct-study reading above.
Human FANCL is UniProt Q9NW38. The literal natural products are Q9NW38-1 (375 residues) and Q9NW38-2 (380 residues, the described insertion at position 178). Processing of the displayed chain to residues 2–375 is distinct from alternative splicing. Engineered RING/URD fragments, catalytic mutants, tags and nonhuman orthologs do not establish identical function or localization of both natural human products. All original product records remain unchanged.
The strongest independently read human substrate experiment is PMID:19589784, official PMC main: Materials and Methods, “Construction of Plasmids,” “Protein Expression and Purification,” and “Ubiquitination Assay”; Results on FANCI monoubiquitination and Figure 4 caption. Baculovirus/Hi5-expressed human GST-FANCL and its C307A mutant are distinguished from human UBE2T/C86A and human FANCI/K523R. The reaction requires ATP, E1, UBE2T and active FANCL. FANCL autoubiquitination is a separate readout. These are direct performed E3 reactions, not merely the requirement for FANCI/FANCD2 as ubiquitination substrates. The main text and caption were read; no new figure pixels or supplemental text were inspected for this paper.
PMID:21775430(https://pubmed.ncbi.nlm.nih.gov/21775430/) provides human-domain structural and biochemical evidence. Read scope: human URD 109–294/RING 289–375 constructs, protein production, thioester assay, substrate pull-downs and UBE2T-binding Results. The human URD does not form an E2-like ubiquitin thioester; human RING binds UBE2T. The FANCD2 substrate is human, whereas the FANCI substrate used in those pull-downs is Xenopus laevis. PMID:24389026(https://pubmed.ncbi.nlm.nih.gov/24389026/) resolves the human RING–human UBE2T interaction, but its executed monoubiquitination assay uses Xenopus tropicalis FANCL and Xenopus laevis FANCD2. These species/preparation boundaries are retained rather than describing every assay as human.
PMID:21229326(https://pubmed.ncbi.nlm.nih.gov/21229326/) uses mouse FANCL/UBE2W constructs. Actual Methods, localization/binding, ubiquitination/discharge Results and Discussion were read. FANCL/PHD-L ubiquitination, FANCL-enhanced UBE2W discharge and polyubiquitin formation in vitro are distinct from human-cell UBE2W depletion after UV. The latter is not a human FANCL perturbation. These observations do not support an absolute claim that FANCL can never facilitate a polyubiquitin reaction; the established FA-substrate process remains monoubiquitination.
PMID:17938197(https://pubmed.ncbi.nlm.nih.gov/17938197/) is chicken DT40 biology: FANCL C305A/C357A mutants retain assembly/chromatin recruitment but fail FANCD2 modification and cisplatin complementation. Methods, corresponding Results and captions were read. Its mammalian-extrapolation caution remains explicit. PMID:25205745(https://pubmed.ncbi.nlm.nih.gov/25205745/) reports the Drosophila Fancl LL00701 mutant and controls; selected strain-generation, sensitivity Methods, Results and Figure 1 caption were read. The tested Fancl phenotype is high-dose nitrogen-mustard sensitivity. The broader MMS/IR/recombination results assigned to Fancm are not transferred to Fancl. The complete cached abstract of PMID:16860002(https://pubmed.ncbi.nlm.nih.gov/16860002/) positively supports fly FANCL RNAi, crosslink sensitivity and FANCD2 monoubiquitination; complete original Methods were not recovered.
The complete cached abstracts of PMID:12973351, PMID:16916645 and PMID:19111657 were read. They positively support the discovery of FANCL as the FA catalytic subunit, UBE2T association and minimal FANCD2 monoubiquitination, respectively. Original full Methods/Results were not recovered here, and no unseen construct/species details are inferred. The historical partner expansion associated with PMID:19111657 remains that source; an earlier acquisition narrative mislabeled it PMID:22343915, while its authoritative source mapping was already correct.
Current official GO definitions support refinement from GO:0004842 to its E3 child GO:0061630, from protein ubiquitination to GO:0006513, and from DNA repair to GO:0036297 for the evidenced repair work. Checked E3 children describing histone-specific or ubiquitin-chain activity are not appropriate replacements for the demonstrated FA-substrate reaction. No nuclease, polymerase or E2 catalytic intermediate is assigned to FANCL. The same precision rule now applies to the experimental DNA-repair and DNA-damage-response annotations: both parent processes remain biologically true, but GO:0036297 supplies the supported specific repair participation. Its checked ancestry includes GO:0006281 and GO:0006974. The refinement uses independently read human FANCL experiments, without pretending that the inaccessible PMID:16916645 main was read or that its UBE2T phenotype was FANCL-specific.
The Human Protein Atlas FANCL subcellular record and official XML were read. HPA036685 is classified as supported, with nuclear-body localization in HEK293/Rh30 and nuclear bodies plus vesicles in U2OS. Actual HEK293 and U2OS images were viewed; Rh30 images were not. The antigen maps to displayed residues 94–174, before the splice insertion. This supports a nuclear pool and a contextual extranuclear pool, without resolving the two natural products, proving exclusive specificity, or identifying the nuclear envelope. HPA036686 supplies an antigen record but no cell-localization data in the inspected XML. Cytoplasm is not narrowed to organelle-excluding cytosol because vesicular localization is also reported. Contextual/non-core does not mean inactive.
Mouse Q9CR14/Fancl nuclear/cytoplasmic assertions trace to PMID:21229326 and actual partner-dependent redistribution of mouse constructs. The separate nuclear-envelope donor traces to PMID:12574169(https://doi.org/10.1074/jbc.M211023200), with GGN/PR:Q80WJ1. The author-uploaded original localization Methods, Results and Figure 6 caption are available and were read; the normal publication cache remains abstract-only. Methods, “Subcellular Localization”: pEGFP-N2/Ggn1 and pcDNA3.1HisC/Pog coexpression in HeLa, with tagged POG detected using anti-Xpress. Results, “GGN1 and GGN3 Determined the Localization of POG in Mammalian Cells,” and Figure 6F–H report POG/GGN1 colocalization in a perinuclear pattern. The Discussion describes localization near the nuclear membrane and proposes GGN1 topology from its sequence and localization.
This is positive conditional mouse localization evidence, but the exact nuclear-envelope compartment remains UNDECIDED for the human orthology inference. Colocalization with GGN1 cannot independently resolve an envelope location when GGN1's own topology is inferred; the experiment does not distinguish an envelope surface from neighboring structures. No transmembrane segment in FANCL is required for peripheral association. GO:0005635 denotes the nuclear double-membrane envelope, whereas GO:0048471 specifically denotes nearby cytoplasm, a compartment that is also unresolved here. Neither an endogenous human localization assay nor equivalence of natural products is established. Figure pixels remain uninspected after a failed author-figure download. This precision reassessment supersedes the previous non-core disposition, while retaining the recovered full-text evidence and its access history.
Fresh official PTHR13206 tree and alignment responses identify the human leaf PTN002491116 in PANTHER v19. Its ungapped 375-residue sequence exactly matches the displayed Q9NW38 sequence. Its path includes PTN000324788 and all four positive IBDs for nucleus, DNA repair, monoubiquitination and E3 ligase activity; no NOT occurs on that path in the saved family PAINT rows. This resolves the earlier six request failures without replacing their records. Human self-WITH is legitimate experimental grounding. The later DNA-repair IBD additionally names Arabidopsis AT5G65740, absent from the current human GOA donor list; that source-version difference remains explicit. Neither donor count nor that difference is treated as weak/circular biology. This placement does not establish function of the 380-residue product.
Mouse Q9CR14 and fly Q8T913 were independently identified and their actual experimental GOA sources inspected. The biological assessment uses the target and donor assays described above rather than family membership alone. Actual IPR026848, EC 2.3.2.27, SL-0191 and SL-0086 were checked. The target matches ARBA00026330 clause 753 (zero-based; three FunFam conditions plus Eukaryota), and ARBA00028366 clauses 2 and 30 (InterPro/Mammalia and the three FunFam conditions). Only these relevant clauses and rule outputs were manually assessed, not every unrelated clause. GO_REF:0000041 explicitly describes the old UniPathway mapping; the resource's discontinued status is retained without treating it as a new experiment.
All 11 originating events were traced through their actual participants to FANCL's own human reference entity. Ten nuclear events use entity 419520/Q9NW38, residues 1–375, with its own nucleoplasm compartment. The PKR-associated model uses entity 420789, residues 1–375, with its own cytosol compartment. There are 26 target routes in total. Each review includes its exact originating event as a bare citation, separate from inherited publication quotations.
| Event | FANCL-specific reading and boundary |
|---|---|
| R-HSA-6785126 | Core assembly: direct input and core-containing output. |
| R-HSA-6785342 | ID2/UBE2T recruitment: target in input/output; independent human RING–UBE2T binding corroborates the named contact. |
| R-HSA-6785361 | Monoubiquitination: target in input/output and composite catalyst; its E3 role is independently demonstrated. |
| R-HSA-6785732 | Nuclease recruitment: target remains in assemblies; no isolated FANCL–nuclease interaction is inferred. |
| R-HSA-6785986 | Unhooking: target is a complex member; nucleases perform incision. |
| R-HSA-6786155 | POLN recruitment: target remains in assemblies; named contacts concern FANCD2/PCNA. |
| R-HSA-6786166 | Translesion synthesis: POLN performs synthesis, despite FANCL in the composite catalyst. |
| R-HSA-6786171 | Deubiquitination: USP1:WDR48 performs cleavage; FANCL remains a distinct E3 component. |
| R-HSA-6788385 | ATR–ATRIP recruitment: reported ATRIP–FANCL contact is model evidence; its primary contact assay was not independently reread. |
| R-HSA-6788392 | ATR phosphorylation: target membership does not confer kinase activity. |
| R-HSA-9835411 | Cytosolic FA-core:HSP70 participant in a PKR model: summation emphasizes FANCC and FANCA/FANCC/FANCG perturbations, not isolated FANCL inhibition. |
The event summations and all FANCL routes were read; not every primary paper cited by these models was reread. Ten linked nuclear events are not ten independent localization experiments. PMID:27986592(https://pubmed.ncbi.nlm.nih.gov/27986592/) independently supports human BL100/CEF assembly through selected actual purification/dropout/XLMS Methods and Results. Its human architecture, Xenopus ID2 structural context and separately cited enzymology remain distinct. FANCL stabilizes the reconstituted assembly but is not assigned isolated dimerization or a new scaffold function.
Two complementary facets of the same ligase mechanism are represented: GO:0061630 ubiquitin protein ligase activity and GO:0031624 ubiquitin conjugating enzyme binding. The second identifies cognate E2 recognition; it does not posit another catalytic pathway or an independent scaffold function. Human FANCL contains an ELF, a central UBC–RWD region and a RING domain. The human central domain is not described using the older Drosophila DRWD interpretation. Its failure to form a ubiquitin thioester distinguishes its recognition role from an E2 intermediate.
Protein monoubiquitination and interstrand cross-link repair capture the performed E3 chemistry and its repair participation. Their typed is_a/part_of GO ancestry does not make one a redundant ancestor of the other. The independently supported nuclear location is used for both core facets; the unresolved source-specific human chromatin context is not silently promoted to a core location. The two old core positions and their four original quotations are retained. New supporting citations contain identifiers without new quotation text.
The literal 375- and 380-residue product objects remain unchanged. The five-residue insertion in the central region motivates a product-specific experimental question; neither family placement nor activity of recombinant displayed-product fragments proves functional equivalence. The inherited ubiquitin-binding assertion remains an ISS proposal supported by conserved ELF evidence. It is separate from RING–UBE2T recognition, remains outside the two core facets, and does not become a human IDA or a new biological-process assertion.
All 91 genuine current imported contexts are represented exactly once, plus inherited NEW 47, giving 92 stored and active objects. The 48 historical positions remain. Grouped screens at positions 10 and 11 retain their first current partner contexts, with other reviewed partners appended. Position 44 retains unresolved UBE2W; the independently supported UBE2T context appends separately. Only the three independently approved record_section metadata properties are added at the unchanged UniProt quotation positions 6, 8 and 44. They do not change quotation text or scientific source identity.
Six overlapping whole-reference assessments retain the old note once and both complete current reading scopes. For PMID:16916645 and PMID:19111657, UNVERIFIED records the uninspected operative evidence while retaining verified identifiers and positive abstracts. It does not allege falsity or override the independent human evidence supporting E3 and UBE2T activity. PMID:12973351 has a broader original direct-study read despite the narrower database assessment; neither scope expands the other.
Explicit full_text_unavailable flags mirror immutable selected normal metadata. External availability, actual selected text and pixel inspection are separate. All 31 original reference identities/findings and 34 quotation/path/reference associations are preserved; eight additional reference identities yield 39 total. The complete 41-source normal union has no conflicting bytes, with 34 selected sources and seven private context records. No publication acquisition or new quotation was required during integration. Status remains DRAFT because three source-specific contexts are unresolved; it does not undo completion of their explicit review.
The DNA-repair IBA precision refinement now includes structured TERM_SCOPING_PROBLEM / GRANULARITY_MISMATCH metadata. Its source entities explicitly SUPPORT_TRANSFER: the broad parent is true, the positive ancestral placement is preserved, and human self-WITH is legitimate. No residue loss, false donor or circular propagation is alleged.