Affinage

SRP9

Signal recognition particle 9 kDa protein · UniProt P49458

Round 2 corrected
Length
86 aa
Mass
10.1 kDa
Annotated
2026-04-28
49 papers in source corpus 18 papers cited in narrative 18 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

SRP9 is a core subunit of the signal recognition particle (SRP) and functions as an obligate heterodimer with SRP14 to bind the Alu domain of 7SL SRP RNA via a conserved alpha-beta-beta-beta-alpha fold (the Alu binding module), presenting a positively charged surface—including critical lysines in the SRP9 alpha2 helix—that contacts ribosomal RNA to mediate translational elongation arrest during co-translational protein targeting to the endoplasmic reticulum (PMID:7518078, PMID:9233785, PMID:20348448). The SRP9/14 heterodimer exists in large cytoplasmic excess over SRP, where it binds Alu-family retrotransposon RNAs and BC200 RNA to form Alu RNPs that inhibit both cap-dependent and IRES-mediated translation initiation by engaging 40S ribosomal subunits and blocking 48S complex assembly (PMID:7542942, PMID:25697503). SRP9/14 localizes to stress granules upon cellular stress and promotes their formation through direct, Alu-RNA-competitive binding to 40S subunits, while a nuclear pool cotranscriptionally regulates 7SL and BC200 RNA expression (PMID:25200073, PMID:37156570). In neurons, SRP9 controls surface trafficking of AMPA receptors via ER-dependent synthesis, and its knockdown reduces febrile seizure susceptibility in mice (PMID:25590037).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1994 High

    Establishing that SRP9 functions as a heterodimer with SRP14 to bind SRP RNA and confer elongation arrest answered the basic question of how the Alu domain contributes to SRP-mediated translation arrest.

    Evidence In vitro reconstitution with single-chain SRP9/14 fusion proteins, SRP RNA binding and cell-free translation/translocation assays

    PMID:7518078

    Open questions at the time
    • Structural basis of heterodimer-RNA interaction unknown at this point
    • Mechanism by which SRP9/14 contacts the ribosome not defined
  2. 1995 High

    The discovery that SRP9/14 exists in >20-fold excess over SRP in primate cells and associates with cytoplasmic Alu RNA in vivo revealed that SRP9/14 has functions beyond SRP assembly, opening the Alu RNP biology field.

    Evidence Immunoprecipitation, sucrose gradient sedimentation, quantitative binding assays with purified protein from HeLa cells

    PMID:7542942 PMID:7730321

    Open questions at the time
    • Functional consequence of Alu RNP formation unknown
    • Whether excess SRP9/14 has additional non-Alu binding partners
  3. 1997 High

    Crystal structure determination of SRP9/14 at 2.5 Å defined the Alu binding module fold and identified the positively charged concave surface predicted to mediate RNA contacts, while mutagenesis of SRP RNA nucleotide G24 and systematic Alu RNA domain mapping established the structural determinants of high-affinity binding.

    Evidence X-ray crystallography, site-directed mutagenesis, quantitative competition binding assays with minimal Alu RNA domains and evolutionary variants

    PMID:9016560 PMID:9032241 PMID:9092618 PMID:9233785 PMID:9409618

    Open questions at the time
    • No co-crystal structure with RNA yet
    • Residue-level contacts between SRP9 and RNA unresolved
  4. 2000 High

    Co-crystal structures of SRP9/14 bound to the 5' and 5'+3' domains of SRP RNA revealed that SRP9/14 recognizes a conserved U-turn in the RNA core and that the 3' domain docks reversibly, providing the first atomic model of the complete Alu domain.

    Evidence X-ray crystallography of SRP9/14–RNA complexes

    PMID:11089964

    Open questions at the time
    • How the Alu domain-ribosome interface mediates elongation arrest remained unresolved
    • Structure not yet placed in ribosome-bound context
  5. 2010 High

    Systematic mutagenesis identified specific basic residues in SRP9 (alpha2 helix lysines) and SRP14 (KRDKK motif) that are essential for elongation arrest, clustering on a positively charged platform that contacts ribosomal RNA, thus defining the molecular mechanism of ribosome engagement.

    Evidence Alanine scanning mutagenesis with cell-free translation and mammalian cell functional assays

    PMID:20348448

    Open questions at the time
    • Direct structural visualization of SRP9/14-ribosome contact not achieved
    • Whether the same surface mediates 40S binding outside SRP context
  6. 2014 High

    Discovery that SRP9/14 directly binds 40S ribosomal subunits independently of Alu RNA, localizes to stress granules, and promotes stress granule formation established a non-SRP cytoplasmic function in translational regulation and stress responses; simultaneously, identification of SRP9 as a febrile seizure susceptibility gene linked it to ER-dependent AMPA receptor trafficking in neurons.

    Evidence siRNA knockdown, 40S binding assays, competitive binding, immunofluorescence, stress granule quantification; QTL mapping, in vivo shRNA in mouse brain, electrophysiology, surface biotinylation

    PMID:25200073 PMID:25590037

    Open questions at the time
    • Binding site of SRP9/14 on 40S subunit not mapped
    • Whether stress granule role is direct or via translational inhibition
    • Mechanism linking SRP9 to specific ER cargo such as GluA1 not fully dissected
  7. 2015 High

    Mechanistic dissection showed Alu RNPs inhibit translation initiation by SRP9/14 binding to 40S and blocking 48S complex formation, with Alu RNA serving as an assembly factor rather than a persistent component, explaining how Alu RNA expression levels tune global translation.

    Evidence Cell-free 48S complex formation assays, 40S binding, reporter assays with Alu RNA overexpression and binding-defective mutants in cells

    PMID:25697503

    Open questions at the time
    • Structural basis of SRP9/14–40S interaction still unresolved
    • In vivo stoichiometry of Alu RNP inhibition not quantified
  8. 2023 Medium

    Identification of a nuclear SRP9/14 pool that cotranscriptionally regulates 7SL and BC200 RNA expression expanded SRP9/14 function to transcriptional regulation, revealing a feedback loop in which SRP9/14 controls the abundance of its own RNA substrates.

    Evidence Immunofluorescence, subcellular fractionation, siRNA knockdown, transcriptional activity assays in MCF-7 cells

    PMID:37156570

    Open questions at the time
    • Mechanism of transcriptional regulation (direct chromatin binding vs. cofactor role) unresolved
    • Not replicated in additional cell types
    • Whether nuclear SRP9/14 exists as heterodimer or monomer unknown
  9. 2025 Medium

    Structural and functional analysis confirmed that the pseudoknot U-turn motif is required for SRP9/14 association with Alu-family RNAs, explaining why divergent Alu elements lose SRP9/14 binding.

    Evidence Co-immunoprecipitation in multiple cell lines, SAXS, site-directed mutagenesis of BC200 RNA

    PMID:40345827

    Open questions at the time
    • Whether loss of SRP9/14 binding alters retrotransposition potential of these elements not tested
    • Solution structure of SRP9/14-bound divergent Alu RNAs lacking U-turn not determined

Open questions

Synthesis pass · forward-looking unresolved questions
  • The structural basis of SRP9/14 binding to the 40S ribosomal subunit—the interface that mediates both translational inhibition and stress granule formation—remains unresolved, as does the mechanism by which nuclear SRP9/14 regulates Pol III transcription.
  • No cryo-EM or crystal structure of SRP9/14 on the 40S subunit
  • Nuclear mechanism (direct DNA/chromatin binding vs. indirect) undefined
  • Relative contributions of SRP vs. Alu RNP functions to cell physiology not quantified in vivo

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 7 GO:0045182 translation regulator activity 4 GO:0005198 structural molecule activity 3
Localization
GO:0005829 cytosol 3 GO:0005840 ribosome 2 GO:0005634 nucleus 1
Pathway
R-HSA-392499 Metabolism of proteins 3 R-HSA-9609507 Protein localization 3 R-HSA-8953854 Metabolism of RNA 1
Partners
BC200 RNARPS6 (40S SUBUNIT)SRP RNA (7SL RNA)SRP14
Complex memberships
Alu RNPBC200 RNPSRP (signal recognition particle)SRP9/14 heterodimer

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 SRP9 and SRP14 form a heterodimer that binds SRP RNA and confers elongation arrest activity to SRP. Single-chain fusion proteins containing both SRP9 and SRP14 sequences in either permutation fold into a heterodimer-like structure, bind SRP RNA as monomers, and reconstitute elongation arrest activity, demonstrating that the normal N- and C-termini of both proteins are dispensable for folding, RNA-binding, and biological activity. In vitro reconstitution with permuted single-chain fusion proteins, SRP RNA binding assays, cell-free translation/translocation assays Nucleic acids research High 7518078
1995 The SRP9/14 heterodimer constitutes the Alu RNA-binding protein (Alu RBP). Human SRP9 together with SRP14 binds the Alu region of 7SL RNA, scAlu RNA, and scB1 RNA with high affinity (Kd values of ~203 pM, 318 pM, and 1.8 nM respectively). The primate-specific C-terminal tail of hSRP14 does not appreciably affect scAlu RNA binding. Quantitative equilibrium binding assays with purified SRP9/14 from HeLa cells; Kd determination The Journal of biological chemistry High 7730321
1995 SRP9/14 is present in more than 20-fold excess over SRP in primate cells and the majority of this excess is cytoplasmic and not bound to SRP RNA. A significant fraction of small cytoplasmic Alu RNA is complexed with SRP9/14 in an 8.5S particle in vivo, indicating SRP9/14 has roles beyond SRP assembly. Antibody characterization, immunoprecipitation, sucrose gradient sedimentation, in vivo analysis of primate vs. rodent cells Molecular biology of the cell High 7542942
1996 Dimeric Alu RNAs induced by adenovirus infection are assembled into SRP9/14-containing RNPs in vivo, while SRP levels remain unchanged. Dimeric Alu RNAs are also associated with the La protein, confirming they are nascent RNA polymerase III transcripts. Immunoprecipitation with anti-SRP9 antiserum from adenovirus-infected HeLa cells, Northern blotting Nucleic acids research Medium 8932367
1997 The crystal structure of the mouse SRP9/14 heterodimer was determined at 2.5 Å resolution. SRP9 and SRP14 are structurally homologous, each containing an alpha-beta-beta-beta-alpha fold designated the 'Alu binding module' (Alu bm). The heterodimer has pseudo 2-fold symmetry and is saddle-shaped with a curved six-stranded amphipathic beta-sheet; the concave surface is lined with positively charged residues predicted to interact with RNA. X-ray crystallography at 2.5 Å resolution The EMBO journal High 9233785
1997 Human SRP9/14 binds with higher affinity than mouse SRP9/14 to all Alu-like RNAs tested, including BC200 RNA, and this difference is not explained by the additional C-terminal domain of anthropoid SRP14. Binding affinity is inversely proportional to evolutionary distance from 7SL RNA. Quantitative in vitro binding assays comparing human and mouse SRP9/14 with multiple Alu-like RNAs Nucleic acids research High 9016560
1997 A minimal Alu RNA folding domain of 86 nucleotides (SA86) was identified that specifically competes with 7SL RNA for SRP9/14 binding. This domain contains two stem-loops connected by a conserved bulge and part of the central adaptor stem, functions as an autonomous RNA folding unit, and does not require free 5' and 3' ends for folding or SRP9/14 recognition, suggesting Alu RNA identity is determined by a characteristic tertiary structure. Quantitative equilibrium competition assays with ribozyme-produced Alu RNA variants; circularly permuted RNA analysis RNA (New York, N.Y.) High 9409618
1997 Mutation of G24 in the Alu domain of SRP RNA to C reduces SRP9/14 binding by at least 50-fold, while A and U substitutions reduce binding ~2- and 5-fold respectively. SRPs reconstituted with mutant RNAs were not significantly defective in translation arrest, indicating G24 mediates high-affinity SRP9/14 binding but does not directly contact the translational machinery. Site-directed mutagenesis of SRP RNA, in vitro SRP reconstitution, translation arrest assays Nucleic acids research High 9092618
1997 Mutations accompanying Alu RNA evolution led to thermodynamic destabilization of the Alu right monomer and decreased its affinity for SRP9/14, while the Alu left monomer maintained structural integrity and high SRP9/14 affinity. Loss of right monomer SRP9/14 affinity correlated with increased scAlu RNA production and coincided with decreased Alu amplification rates during primate evolution. In vitro binding assays with evolutionary Alu RNA variants, structural analysis, in vivo retrotransposition analysis Molecular and cellular biology High 9032241
1998 SRP9/14 heterodimer is an integral component of the neuronal BC200 RNP in primate brain. A protein immunoreactive with anti-SRP9 antibodies co-immunoprecipitates with BC200 RNA in vivo, indicating SRP9/14 binding to the Alu-homologous 5' domain of BC200 RNA. This suggests the BC200 RNP may regulate translation in dendrites via an SRP-like translation arrest mechanism. Immunoprecipitation with anti-SRP9 antibodies from primate brain tissue Neuroscience letters Medium 9605471
2000 Crystal structures of the SRP9/14 heterodimer bound to the 5' domain alone and to a construct containing both 5' and 3' domains of SRP RNA were determined. SRP9/14 binds strongly to the conserved core of the 5' domain forming a U-turn connecting two helical stacks. The 3' domain docks reversibly and more weakly. A complete Alu domain model is presented consistent with extensive biochemical data, suggesting the Alu domain structure is conserved in Alu retrotransposition intermediates. X-ray crystallography of SRP9/14-RNA complexes Nature High 11089964
2010 Mutational analysis identified two patches of basic residues in SRP9/14 essential for elongation arrest activity: the KRDKK pentapeptide of SRP14 (replaceable by four lysines) and three lysines in the solvent-accessible alpha2 helix of SRP9. All essential residues cluster on one face of SRP9/14 forming a positively charged platform, suggesting they interact with ribosomal RNA via electrostatic contacts with the phosphate backbone. The SRP14 internal loop is dispensable. Alanine scanning mutagenesis of hSRP9/14, cell-free translation/translocation assays, mammalian cell functional assays RNA (New York, N.Y.) High 20348448
2014 SRP9/14, but not SRP, localizes to stress granules (SGs) following arsenite or hippuristanol treatment. SRP9/14 directly binds to 40S ribosomal subunits independently of Alu RNA, and this binding is mutually exclusive with Alu RNA binding. Depletion of SRP9/14 decreases SG size and the number of SG-positive cells. Alu RNA competitively regulates SRP9/14 binding to 40S; increasing cytoplasmic Alu RNA promotes SG disassembly by disengaging SRP9/14 from 40S. Immunofluorescence, siRNA knockdown, overexpression, direct 40S binding assays, competitive binding assays in human cells Nucleic acids research High 25200073
2014 Srp9 was identified as a febrile seizure susceptibility gene. In vivo knockdown of brain Srp9 reduced febrile seizure susceptibility in mice and was accompanied by reduced hippocampal AMPA and NMDA currents. Downregulation of neuronal Srp9 reduced surface expression of AMPA receptor subunit GluA1, indicating SRP9 conveys its effects through ER-dependent synthesis and trafficking of membrane proteins such as glutamate receptors. QTL mapping, in vivo shRNA knockdown in mouse brain, electrophysiology (patch-clamp), surface biotinylation assays for GluA1 Annals of clinical and translational neurology High 25590037
2015 Alu RNPs inhibit translation initiation by direct binding of SRP9/14 to 40S ribosomal subunits; Alu RNA acts as an assembly factor for this interaction but continuous association with 40S is not required for inhibition. Binding of SRP9/14 to 40S prevents 48S complex formation by interfering with mRNA recruitment. Both cap-dependent and IRES-mediated initiation are inhibited. In cells, Alu RNA overexpression decreases translation of reporter mRNAs, and this is alleviated by a mutation reducing Alu RNA affinity for SRP9/14. Cell-free translation assays, 40S binding assays, 48S complex formation assays, reporter assays in cells with Alu RNA overexpression and binding-defective mutants Nucleic acids research High 25697503
2023 SRP9/14 has a distinct nuclear localization in MCF-7 cells and transcriptionally regulates 7SL and BC200 RNA expression. Under SRP9/14 knockdown, 7SL and BC200 RNA steady-state levels and transcriptional activity are altered, establishing a novel cotranscriptional regulatory function for nuclear SRP9/14. Immunofluorescence, subcellular fractionation, siRNA knockdown, RNA steady-state and decay measurements, transcriptional activity assays RNA (New York, N.Y.) Medium 37156570
2025 The Alu domain of SRP RNA, through its interactions with SRP9 and SRP14 proteins, is sufficient for targeting SRP RNAs to lysosomes for degradation in an autophagy-dependent manner, establishing SRP9/14 as a mediator of selective lysosomal RNA targeting. Lysosomal RNA profiling, autophagy perturbation experiments, domain deletion/sufficiency assays bioRxivpreprint Medium bio_10.1101_2025.09.09.674968
2025 A short human Alu RNA (EB120) that lacks the canonical U-turn nucleotide triad within its pseudoknot domain fails to associate with SRP9/14 in a cellular context. Mutation of a critical guanosine in the U-turn motif of BC200 significantly reduces BC200 expression. Small-angle X-ray scattering shows EB120 lacks the canonical Alu RNA fold, establishing that the pseudoknot U-turn structure is required for SRP9/14 association. Co-immunoprecipitation in multiple cell lines, SAXS structural analysis, site-directed mutagenesis, expression analysis in 18 cell lines/tissues RNA (New York, N.Y.) Medium 40345827

Source papers

Stage 0 corpus · 49 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2005 Nucleolar proteome dynamics. Nature 934 15635413
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2007 Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular systems biology 733 17353931
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2015 Widespread macromolecular interaction perturbations in human genetic disorders. Cell 454 25910212
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2015 A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell 433 26638075
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nature methods 370 26414014
2007 Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS genetics 325 17500595
2012 A high-throughput approach for measuring temporal changes in the interactome. Nature methods 273 22863883
2017 Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature communications 221 28524877
2013 Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nature methods 170 23455922
2020 UFMylation maintains tumour suppressor p53 stability by antagonizing its ubiquitination. Nature cell biology 168 32807901
2019 H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. Nature cell biology 162 30804502
2019 A protein-interaction network of interferon-stimulated genes extends the innate immune system landscape. Nature immunology 159 30833792
2000 Structure and assembly of the Alu domain of the mammalian signal recognition particle. Nature 152 11089964
2020 Comparative Application of BioID and TurboID for Protein-Proximity Biotinylation. Cells 146 32344865
2019 Mapping the proximity interaction network of the Rho-family GTPases reveals signalling pathways and regulatory mechanisms. Nature cell biology 137 31871319
2014 The central role of EED in the orchestration of polycomb group complexes. Nature communications 131 24457600
2013 A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. PLoS genetics 131 23349634
2013 Proteomic analysis of podocyte exosome-enriched fraction from normal human urine. Journal of proteomics 126 23376485
2023 The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation. Science (New York, N.Y.) 117 37616343
2011 Host cell interactome of HIV-1 Rev includes RNA helicases involved in multiple facets of virus production. Molecular & cellular proteomics : MCP 114 22174317
2008 Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. Journal of proteome research 89 18549262
1995 The SRP9/14 subunit of the signal recognition particle (SRP) is present in more than 20-fold excess over SRP in primate cells and exists primarily free but also in complex with small cytoplasmic Alu RNAs. Molecular biology of the cell 53 7542942
1996 Crystallization and preliminary X-ray analysis of the 9 kDa protein of the mouse signal recognition particle and the selenomethionyl-SRP9. FEBS letters 52 8617357
1996 Monomeric scAlu and nascent dimeric Alu RNAs induced by adenovirus are assembled into SRP9/14-containing RNPs in HeLa cells. Nucleic acids research 49 8932367
1995 Human signal recognition particle (SRP) Alu-associated protein also binds Alu interspersed repeat sequence RNAs. Characterization of human SRP9. The Journal of biological chemistry 48 7730321
1997 The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14. The EMBO journal 46 9233785
1997 The SRP9/14 subunit of the human signal recognition particle binds to a variety of Alu-like RNAs and with higher affinity than its mouse homolog. Nucleic acids research 45 9016560
1997 The decline in human Alu retroposition was accompanied by an asymmetric decrease in SRP9/14 binding to dimeric Alu RNA and increased expression of small cytoplasmic Alu RNA. Molecular and cellular biology 40 9032241
2010 Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein. RNA (New York, N.Y.) 38 20348448
1998 Heterodimer SRP9/14 is an integral part of the neural BC200 RNP in primate brain. Neuroscience letters 37 9605471
2015 Alu RNA regulates the cellular pool of active ribosomes by targeted delivery of SRP9/14 to 40S subunits. Nucleic acids research 33 25697503
2014 Direct binding of the Alu binding protein dimer SRP9/14 to 40S ribosomal subunits promotes stress granule formation and is regulated by Alu RNA. Nucleic acids research 31 25200073
1997 Identification of a minimal Alu RNA folding domain that specifically binds SRP9/14. RNA (New York, N.Y.) 29 9409618
1997 A highly conserved nucleotide in the Alu domain of SRP RNA mediates translation arrest through high affinity binding to SRP9/14. Nucleic acids research 25 9092618
1994 The heterodimeric subunit SRP9/14 of the signal recognition particle functions as permuted single polypeptide chain. Nucleic acids research 23 7518078
2014 Identification of Srp9 as a febrile seizure susceptibility gene. Annals of clinical and translational neurology 15 25590037
2024 The role of SRP9/SRP14 in regulating Alu RNA. RNA biology 5 39563162
2023 Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression. RNA (New York, N.Y.) 5 37156570
2025 Alu RNA pseudoknot alterations influence SRP9/SRP14 association. RNA (New York, N.Y.) 0 40345827