Affinage

SLF1

SMC5-SMC6 complex localization factor protein 1 · UniProt Q9BQI6

Length
1058 aa
Mass
121.0 kDa
Annotated
2026-04-28
11 papers in source corpus 10 papers cited in narrative 10 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

Human SLF1 (SMC5/6 localization factor 1) is a multi-domain adaptor protein that recruits the SMC5/6 complex to DNA damage sites and stalled replication forks through coordinated recognition of phosphorylated RAD18 and nascent chromatin. Its tandem BRCT domain binds RAD18 phosphorylated at S442/S444 in a structurally unique manner involving dual phosphoserine recognition and an α-helical RAD18 element, and this phosphorylation-dependent interaction is required for SLF1 accumulation at DNA lesions and for UV-induced DNA damage repair (PMID:22036607, PMID:37748650). Its ankyrin repeat domain reads unmethylated histone H4 tails on nascent nucleosomes, while a DNA-binding surface overlapping the RAD18-binding interface further enhances nucleosome association, together enabling SLF1—in complex with SLF2—to bridge RAD18-marked damage sites with chromatin-bound SMC5/6 (PMID:39360622). The SLF1/SLF2 subcomplex functions specifically in chromosomal DNA lesion repair and is dispensable for SMC5/6-mediated extrachromosomal DNA silencing, which instead requires the mutually exclusive SIMC1-SLF2 subcomplex (PMID:39360622).

Mechanistic history

Synthesis pass · year-by-year structured walk · 5 steps
  1. 2005 Medium

    Identifying SLF1 as a RAD18-interacting nuclear protein established that it operates in the DNA damage response pathway and localized it to the nucleus and centrosome.

    Evidence Yeast two-hybrid, co-immunoprecipitation, and fluorescence microscopy in human cells with domain truncations

    PMID:15632077

    Open questions at the time
    • Interaction detected by Y2H and single-direction Co-IP; reciprocal validation limited
    • Functional consequence of SLF1–RAD18 interaction for DNA repair not yet tested
    • Identity of the kinase phosphorylating RAD18 at the SLF1-binding site unknown
  2. 2011 High

    Demonstrating that the SLF1–RAD18 interaction is phosphorylation-dependent and required for SLF1 recruitment to damage sites and UV repair defined SLF1 as a damage-responsive effector downstream of RAD18 phosphorylation, separate from RAD18's role in PCNA ubiquitination.

    Evidence Phospho-dependent co-IP with serine mutants, laser micro-irradiation focus formation, siRNA knockdown with UV sensitivity in human cells

    PMID:22036607

    Open questions at the time
    • Kinase responsible for RAD18 S442/S444 phosphorylation not identified
    • Downstream effector recruited by SLF1 at damage sites not yet known
    • Structural basis for phospho-dependent recognition unresolved
  3. 2023 High

    Solving the crystal structure of SLF1 tBRCT bound to phospho-RAD18 revealed a dual-phosphoserine recognition mechanism with a unique α-helical RAD18 element, explaining the specificity of the phospho-dependent interaction.

    Evidence X-ray crystallography of SLF1 tBRCT–RAD18 phosphopeptide complex with biochemical binding assays and structure-guided mutagenesis

    PMID:37748650

    Open questions at the time
    • How SLF1 engagement with RAD18 is coordinated with chromatin binding in vivo unknown
    • Contribution of chromatin context (nucleosome state) to SLF1 recruitment not addressed
  4. 2024 High

    Structural determination of SLF1's ankyrin repeat domain bound to unmethylated H4 tail, together with identification of a DNA-binding surface overlapping the RAD18-binding interface, established a multi-valent chromatin-reading mechanism by which SLF1 bridges phospho-RAD18, nascent nucleosomes, and the SMC5/6 complex via SLF2.

    Evidence X-ray crystallography of ankyrin–H4 complex, structure-based mutagenesis, biochemical binding assays for DNA and nucleosome substrates

    PMID:39360622

    Open questions at the time
    • In vivo reconstitution of the full SLF1–SLF2–SMC5/6 loading pathway at replication forks not performed
    • Whether SLF1 reads H4 methylation status dynamically during replication-coupled repair is untested
    • Regulation of SLF1 itself (post-translational modifications, turnover) largely uncharacterized
  5. 2025 Medium

    Establishing that SLF1/SLF2 and SIMC1-SLF2 are mutually exclusive SMC5/6 subcomplexes with distinct functions—chromosomal DNA repair versus extrachromosomal DNA silencing—resolved how SMC5/6 is differentially targeted to its diverse substrates.

    Evidence (preprint) Genetic depletion, transcriptional reporter assays, and focus-formation microscopy in human cells

    PMID:bio_10.1101_2025.03.27.645818

    Open questions at the time
    • Preprint not yet peer-reviewed
    • Mechanism governing exclusive assembly of SLF1- versus SIMC1-containing subcomplexes unknown
    • Whether SLF1/SLF2 has additional substrates beyond chromosomal DNA lesions not explored

Open questions

Synthesis pass · forward-looking unresolved questions
  • The kinase(s) that phosphorylate RAD18 at S442/S444 to trigger SLF1 recruitment remain unidentified, and how SLF1-mediated SMC5/6 loading is coordinated with replication fork dynamics in vivo has not been reconstituted.
  • Identity of the RAD18 S442/S444 kinase unknown
  • No reconstitution of SLF1-dependent SMC5/6 loading on replicated chromatin templates
  • Post-translational regulation of SLF1 itself uncharacterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 2 GO:0003677 DNA binding 1 GO:0042393 histone binding 1
Localization
GO:0005634 nucleus 2 GO:0005694 chromosome 2
Pathway
R-HSA-73894 DNA Repair 2
Partners
RAD18SLF2SMC5SMC6
Complex memberships
SLF1/SLF2-SMC5/6

Evidence

Reading pass · 10 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 Human BRCTx (SLF1) binds to the C-terminus of hRAD18 as demonstrated by yeast two-hybrid and co-immunoprecipitation assays, and colocalizes with RAD18 in the nucleus. The BRCT domain of BRCTx mediates its localization to the nucleus and centrosome in interphase cells. Yeast two-hybrid, co-immunoprecipitation, fluorescence microscopy, domain mutagenesis Molecular and cellular biology Medium 15632077
2011 RAD18 interacts with BRCTx (SLF1) in a phosphorylation-dependent manner via conserved serine residues on the RAD18 C-terminus, and this interaction is required for BRCTx accumulation at DNA damage sites and for UV-induced DNA damage repair, but not for PCNA mono-ubiquitination or homologous recombination. Co-immunoprecipitation, phosphorylation-dependent interaction assays, laser micro-irradiation/focus formation, siRNA knockdown with UV sensitivity assays DNA repair High 22036607
2023 Crystal structure of SLF1 tandem BRCT repeat (tBRCT) bound to a RAD18 phosphopeptide reveals that SLF1tBRCT recognizes two phosphoserines and adjacent residues in RAD18 for high-affinity binding, including a unique interaction with an α-helical structure in RAD18 not observed in other tBRCT-bound ligands. X-ray crystallography, biochemical binding assays, structure-based mutagenesis The Journal of biological chemistry High 37748650
2024 Crystal structure of SLF1's ankyrin repeat domain bound to unmethylated histone H4 tail shows how SLF1 reads nascent nucleosomes. Structure-based mutagenesis confirmed phosphorylation-dependent interaction between SLF1's tBRCT domain and phosphorylated RAD18 C-terminus (S442 and S444). SLF1's RAD18-binding interface also has DNA-binding activity, providing an additional mechanism to enhance nucleosome binding. SLF1 facilitates SMC5/6 complex recruitment to DNA damage sites through interactions with SLF2, RAD18, and nucleosomes. X-ray crystallography, structure-based mutagenesis, biochemical binding assays Nucleic acids research High 39360622
2025 Human SMC5/6 is regulated by two mutually exclusive subcomplexes—SIMC1-SLF2 and SLF1/2. SLF1/2 is dispensable for SMC5/6-mediated repression of plasmid transcription (ecDNA silencing), while SIMC1-SLF2 is required; conversely, SLF1/2 participates in SMC5/6 recruitment to chromosomal DNA lesions. Genetic depletion, transcriptional reporter assays, fluorescence microscopy of focus formation bioRxivpreprint Medium bio_10.1101_2025.03.27.645818
1996 Yeast Slf1 (S. cerevisiae) participates in a copper homeostasis pathway distinct from Cup1 detoxification, facilitating copper sulfide (CuS) biomineralization on the cell surface. Disruption of SLF1 prevents cells from depleting Cu ions from growth medium and eliminates CuS-dependent brownish coloration; overexpression enhances Cu depletion and CuS deposition. Multicopy suppressor screen, gene disruption, copper sensitivity assays, colorimetric analysis, ion depletion assays Molecular and cellular biology Medium 8628314
2012 Yeast LARP Slf1p associates with hundreds of mRNAs including transcripts encoding copper homeostasis factors, as shown by RIP-Chip. Mutations in the conserved aromatic patch of the La-motif (LAM) impair mRNA association and abolish Slf1-mediated copper resistance. Slf1p stabilizes copper-related mRNA targets in a LAM-dependent manner. RIP-Chip (RNA-binding protein immunopurification-microarray), LAM domain mutagenesis, mRNA stability assays, copper sensitivity assays RNA (New York, N.Y.) Medium 22271760
2023 Yeast Slf1p (LARP) binds within coding regions of highly translated antioxidant enzyme mRNAs at positions framed by ribosome footprints, interacts with both monosomes and disomes after RNase treatment, and deletion of slf1 reduces disome enrichment during oxidative stress and alters programmed ribosome frameshifting rates. Slf1 is proposed to stabilize stalled/collided ribosomes to maintain translation of stress-responsive mRNAs. CLIP/footprinting, ribosome fractionation, disome analysis, frameshifting reporters, genetic KO with polysome profiling Nucleic acids research Medium 37070186
2025 NMR spectroscopy, calorimetry, and MD simulations show that the La-motif (LaM) domain of yeast Slf1 binds RNA with micromolar affinity including poly(A), and that the RNA-binding platform undergoes conformational sampling on the micro-to-millisecond timescale. A Q278A mutation in the aromatic patch destabilizes RNA binding both experimentally and in simulations. NMR spectroscopy, isothermal titration calorimetry, molecular dynamics simulations, mutagenesis Journal of molecular biology Medium 41223936
2014 Fission yeast Slf1 (S. pombe) acts as a membrane anchor for Skb1 at cortical nodes. Slf1 interacts with Skb1 to form megadalton cortical node structures anchored to the plasma membrane via a lipid-binding region in the Slf1 C-terminus. Slf1 is a limiting factor for node formation. Quantitative fluorescence microscopy, in vitro binding assays, lipid-binding domain characterization, genetic quantification of node number Molecular biology of the cell Medium 25009287

Source papers

Stage 0 corpus · 11 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1996 Identification of SLF1 as a new copper homeostasis gene involved in copper sulfide mineralization in Saccharomyces cerevisiae. Molecular and cellular biology 38 8628314
2011 Repression of mitochondrial translation, respiration and a metabolic cycle-regulated gene, SLF1, by the yeast Pumilio-family protein Puf3p. PloS one 31 21655263
2012 La-motif-dependent mRNA association with Slf1 promotes copper detoxification in yeast. RNA (New York, N.Y.) 23 22271760
2023 Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs. Nucleic acids research 13 37070186
2005 BRCTx is a novel, highly conserved RAD18-interacting protein. Molecular and cellular biology 11 15632077
2011 RAD18-BRCTx interaction is required for efficient repair of UV-induced DNA damage. DNA repair 10 22036607
2014 Megadalton-node assembly by binding of Skb1 to the membrane anchor Slf1. Molecular biology of the cell 7 25009287
2023 Structural insights into Rad18 targeting by the SLF1 BRCT domains. The Journal of biological chemistry 4 37748650
2024 Structural mechanisms of SLF1 interactions with Histone H4 and RAD18 at the stalled replication fork. Nucleic acids research 3 39360622
2021 SLF1 polymorphism predicts response to oxaliplatin-based adjuvant chemotherapy in patients with colon cancer. American journal of cancer research 2 33948371
2025 RNA Binding by the Yeast Slf1 and Sro9 La-motif Domains. Journal of molecular biology 0 41223936