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Showing WBP4 — FBP21 is a alias.

WBP4

WW domain-binding protein 4 · UniProt O75554

Length
376 aa
Mass
42.5 kDa
Annotated
2026-06-11
28 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: tie faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

WBP4 (FBP21) is a spliceosomal protein that acts as an activator of pre-mRNA splicing and engages the early spliceosome as a multivalent scaffold for proline-rich spliceosomal partners (PMID:9724750, PMID:19592703). It associates with U2 snRNPs in spliceosomal complex A and localizes to nuclear speckles, where it directly contacts the U1 snRNP protein U1C, the Sm core proteins SmB/B', and the branchpoint-binding protein SF1/mBBP, positioning it to bridge U1 and U2 snRNPs across the intron (PMID:9724750). Recognition of partners is mediated by two tandem WW domains connected by a flexible linker that recognize PPLP (group II) and Pro-Arg/PPR (group III) proline-rich motifs through XP and XP2 grooves, with the bivalent architecture conferring high avidity yet a delocalized, fast-exchanging binding mode toward ligands including SIPP1, SF3B4, and SmB/B' (PMID:10744724, PMID:19592703, PMID:21917930, PMID:35347992). Beyond this scaffolding role, an intrinsically disordered C-terminal region of FBP21 wraps around the C-terminal Sec63 unit of the Brr2 RNA helicase, adopting an extended conformation upon binding that allosterically inhibits helicase activity and, together with direct binding to U4/U6 di-snRNA, restrains U4/U6 unwinding (PMID:28838205, PMID:30558886). Cryo-EM structures of human spliceosomal B complexes place FBP21 at the U6/5' splice-site helix, contacting SNU23 and PRP38 and competing with C9ORF78 for the same Brr2 site (PMID:35241646, PMID:38383864). WBP4 also functions outside splicing as an interactant of the vitamin D receptor, controlling its cytosolic localization (PMID:33288743). Bi-allelic loss-of-function variants in WBP4 abolish the protein and cause widespread mis-splicing underlying a neurodevelopmental syndrome (PMID:37963460).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1998 High

    Established WBP4/FBP21 as a bona fide component of the early spliceosome and proposed a cross-intron bridging function, answering where in the splicing pathway the protein acts.

    Evidence Spliceosomal complex A purification, co-immunoprecipitation, direct binding assays, and speckle colocalization in human cells

    PMID:9724750

    Open questions at the time
    • Did not define the structural basis of partner recognition
    • Functional contribution to splicing not yet demonstrated
  2. 2000 Medium

    Defined the ligand-recognition specificity of the FBP21 WW domains, showing they recognize a distinct Pro-Arg (PPR) class of proline-rich motifs unaffected by arginine methylation.

    Evidence Oriented peptide library screening and in vitro binding with methylated vs. unmethylated peptides, including Sam68

    PMID:10744724 PMID:10748127

    Open questions at the time
    • In vitro peptide binding; physiological relevance of Sam68 interaction not established
    • No structural model of the domain-ligand complex
  3. 2009 High

    Demonstrated FBP21 is a splicing activator in vivo and provided the structural mechanism by which tandem WW domains achieve high-affinity multivalent binding via a flexible linker.

    Evidence NMR solution structure of tandem WW domains, ITC, mutagenesis, and in vivo splicing assay with SIPP1

    PMID:19592703

    Open questions at the time
    • Did not establish full repertoire of in vivo ligands
    • Did not address regulation of helicase steps
  4. 2011 High

    Extended the partner repertoire (SF3B4) and showed the multivalent WW binding mode is semispecific with fast ligand exchange, reframing FBP21 as a delocalized molecular hub rather than a tight-binding adaptor.

    Evidence FRET in nuclear speckles, ITC, and NMR; complemented by phage-display identification of FBP21 WW domains as a borrelidin target with VEGF isoform splicing effects

    PMID:21917930 PMID:22822423

    Open questions at the time
    • How semispecific binding translates to splice-site selection unknown
    • VEGF splicing effect is a single overexpression study
  5. 2017 High

    Revealed a regulatory function beyond scaffolding: the disordered C-terminus binds the Brr2 Sec63 unit and, with U4/U6 di-snRNA binding, allosterically inhibits helicase-driven unwinding.

    Evidence Yeast two-hybrid, biochemical and biophysical binding assays, helicase activity assay, and RNA interaction assay

    PMID:28838205

    Open questions at the time
    • Functional consequence of helicase inhibition for splicing kinetics in cells not resolved
    • Structural detail of the bound complex not yet defined
  6. 2018 High

    Resolved how a disordered region encodes a specific interaction, showing the FBP21 C-terminus folds into an extended conformation on Brr2-Sec63 while retaining dynamics, with charged motifs steering complex formation.

    Evidence NMR spectroscopy and fragment docking with experimental restraints

    PMID:30558886

    Open questions at the time
    • Did not place the interaction in the assembled spliceosome
    • Affinity contribution to helicase regulation in vivo unmeasured
  7. 2020 Medium

    Identified a splicing-independent role for WBP4 as a vitamin D receptor interactant that controls VDR cytosolic localization, broadening the protein's functional scope.

    Evidence Co-immunoprecipitation, subcellular fractionation, and an in vivo vitamin D-intoxicated mouse model with target-gene and serum calcium readouts

    PMID:33288743

    Open questions at the time
    • Whether VDR binding uses the WW domains or disordered region not defined
    • Single lab; mechanism of cytosolic sequestration unresolved
  8. 2022 High

    Cryo-EM and NMR/simulation work positioned FBP21 within the assembled B complex at the U6/5' splice-site helix and showed its tandem WW domains bind SmB/B' in alternative orientations, explaining structural plasticity.

    Evidence Cryo-EM of spliceosomal B complex dimers; molecular dynamics, NMR, and peptide docking of WW-SmB/B'

    PMID:35241646 PMID:35347992

    Open questions at the time
    • Mutual exclusivity with C9ORF78 not mechanistically tied to splicing outcome
    • Dynamics of WW orientation switching in the full spliceosome unknown
  9. 2023 Medium

    Established WBP4 as essential for normal human splicing in vivo by linking complete loss of protein to shared mis-splicing and a neurodevelopmental syndrome.

    Evidence Immunoblotting of patient fibroblasts, RNA sequencing of patient samples, and genetic analysis across multiple families

    PMID:37963460

    Open questions at the time
    • Causal mis-spliced targets driving phenotype not pinpointed
    • Rescue of splicing defects by WBP4 re-expression not shown
  10. 2024 High

    High-resolution human B-complex cryo-EM refined the specific molecular contacts of FBP21 with SNU23, PRP38, and the U6/5' splice-site helix.

    Evidence Cryo-EM structure determination of human spliceosomal B complex dimers

    PMID:38383864

    Open questions at the time
    • How these contacts couple to catalytic activation steps not resolved
    • Order of FBP21 release relative to Brr2 activation undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How FBP21's multivalent semispecific scaffolding and Brr2 inhibition are coordinated to control specific splice-site choice, and which mis-spliced transcripts cause the neurodevelopmental phenotype, remain open.
  • No defined transcriptome-wide rules linking FBP21 occupancy to splice-site selection
  • Causal disease-relevant splicing targets unidentified
  • Interplay between splicing role and VDR localization role unexplored

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0045182 translation regulator activity 2 GO:0098772 molecular function regulator activity 2 GO:0003723 RNA binding 1
Localization
GO:0005654 nucleoplasm 2 GO:0005829 cytosol 1
Pathway
R-HSA-8953854 Metabolism of RNA 3 R-HSA-74160 Gene expression (Transcription) 2
Partners
BRR2PRP38SF1SF3B4SNRPBSNU23U1CVDR
Complex memberships
spliceosome (complex A / B complex)

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 FBP21 (WBP4) is present in highly purified spliceosomal complex A, is associated with U2 snRNPs, and colocalizes with splicing factors in nuclear speckle domains. FBP21 interacts directly with the U1 snRNP protein U1C, the core snRNP proteins SmB and SmB', and the branchpoint binding protein SF1/mBBP, suggesting a role in cross-intron bridging of U1 and U2 snRNPs. Biochemical purification of spliceosomal complex A, co-immunoprecipitation, direct binding assays, immunofluorescence colocalization Proceedings of the National Academy of Sciences of the United States of America High 9724750
2000 The WW domains of FBP21 recognize proline-rich motifs on Sam68 (a Pro-Arg motif class), and asymmetrical dimethylation of arginine residues flanking these motifs has no effect on WW domain binding (in contrast to SH3 domains which are inhibited by such methylation). In vitro binding experiments with methylated vs. unmethylated peptides/proteins, oriented peptide library screening The Journal of biological chemistry Medium 10744724 10748127
2000 FBP21 WW domains belong to the Pro-Arg (PPR) class of WW domain ligand recognition, distinct from PPXY and PPLP classes, as determined by oriented peptide library screening and in vitro binding experiments. Oriented peptide library screening, expression cloning, in vitro binding experiments The Journal of biological chemistry Medium 10744724
2009 FBP21 is an activator of pre-mRNA splicing in vivo, and its splicing activation function and interaction with the splicing factor SIPP1 are both mediated by the two tandem WW domains. The solution structure of the tandem WW domains reveals they recognize both PPLP (group II) and PPR (group III) motifs via XP and XP2 grooves. The highly flexible linker between the tandem WW domains enables simultaneous interaction with two proline-rich motifs of SIPP1, explaining the high-affinity interaction through avidity. NMR structure determination, in vivo splicing assay, mutagenesis, ITC binding measurements The Journal of biological chemistry High 19592703
2011 FBP21 tandem WW domains interact with multiple proline-rich motif-containing spliceosomal proteins, including the newly identified binding partner SF3B4. FRET analysis shows FBP21 interacts with SF3B4 in nuclear speckles. ITC and NMR demonstrate that multivalent binding through tandem WW domains and multiple ligand motifs enhances affinity, but ligand exchange remains fast on the NMR timescale, suggesting a delocalized, semispecific binding mode. FRET, isothermal titration calorimetry (ITC), NMR, proteome interaction analysis The Journal of biological chemistry High 21917930
2011 FBP21 WW domains are a molecular target of borrelidin; binding of borrelidin to FBP21 WW domains alters the ratio of VEGF isoforms toward anti-angiogenic forms. Overexpression of FBP21 in RPE cells shifts VEGF splicing toward pro-angiogenic isoforms, implicating FBP21 in alternative splicing regulation. Phage display affinity biopanning, in vitro binding with recombinant WW domains, transfection/overexpression with RT-PCR splicing assay Chemical science Medium 22822423
2017 An intrinsically disordered C-terminal region of FBP21 binds to the C-terminal Sec63 unit of Brr2 RNA helicase; this interaction allosterically inhibits Brr2 helicase activity. Additionally, FBP21 directly interacts with U4/U6 di-snRNA, reducing the pool of unwound U4/U6 di-snRNA. Yeast-two-hybrid screen, biochemical binding assays, biophysical analyses, helicase activity assay, RNA interaction assay Nucleic acids research High 28838205
2018 The 50 C-terminal residues of FBP21 are intrinsically disordered in the unbound state but adopt an extended conformation upon binding to the C-terminal Sec63 unit of Brr2, covering a large binding surface. Short charged motifs steer complex formation while the bound state retains conformational dynamics. NMR spectroscopy, fragment docking with experimental restraints Biophysical journal High 30558886
2020 WBP4 was identified as a new interactant of the vitamin D receptor (VDR) and controls VDR subcellular localization. The vitamin D antagonist ZK168281 enhances the WBP4-VDR interaction in the cytosol, promoting cytosolic sequestration of VDR and normalizing VDR target gene expression and serum calcium levels in vitamin D-intoxicated mice. Co-immunoprecipitation, subcellular fractionation/localization assay, mouse in vivo treatment model with gene expression analysis Nature communications Medium 33288743
2022 Cryo-EM structures of spliceosomal B complex dimers reveal that FBP21 wraps around the C-terminal helicase cassette of BRR2 and interacts with the U6/5' splice site helix and with SNU23 and PRP38; C9ORF78 and FBP21 bind BRR2 in a mutually exclusive manner at the same site. Cryo-EM structure determination of spliceosomal B complex dimers Nature communications High 35241646
2022 The tandem WW domain of FBP21 can bind its natural ligand SmB/B' peptide in two different orientations (parallel and antiparallel), with the relative orientation of the two WW domains adapting accordingly, as characterized by NMR and molecular simulations. Molecular dynamics simulations, NMR experiments, peptide docking, density-based clustering Journal of chemical information and modeling Medium 35347992
2024 Cryo-EM analyses of human spliceosomal B complexes provide new insights into how FBP21 interacts with SNU23 and PRP38 and the U6/5' splice site helix, revealing its specific molecular contacts within the B complex. Cryo-EM structure determination of human spliceosomal B complex dimers The EMBO journal High 38383864
2023 Bi-allelic loss-of-function variants in WBP4 cause complete loss of protein (confirmed by immunoblotting) and result in shared abnormal splicing patterns—including mis-splicing of genes associated with nervous system abnormalities—underlying a neurodevelopmental syndrome, establishing WBP4 as essential for normal splicing in vivo. Immunoblotting on patient fibroblasts, RNA sequencing of patient samples, genetic analysis American journal of human genetics Medium 37963460

Source papers

Stage 0 corpus · 28 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2000 Arginine methylation inhibits the binding of proline-rich ligands to Src homology 3, but not WW, domains. The Journal of biological chemistry 207 10748127
1998 WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proceedings of the National Academy of Sciences of the United States of America 139 9724750
2012 A genome-wide association study identifies 2 susceptibility Loci for Crohn's disease in a Japanese population. Gastroenterology 113 23266558
2000 A novel pro-Arg motif recognized by WW domains. The Journal of biological chemistry 69 10744724
2015 Genetic characteristics of inflammatory bowel disease in a Japanese population. Journal of gastroenterology 44 26511940
2004 Identification and characterization of human DIAPH3 gene in silico. International journal of molecular medicine 43 14767582
2009 Structure and function of the two tandem WW domains of the pre-mRNA splicing factor FBP21 (formin-binding protein 21). The Journal of biological chemistry 39 19592703
2011 Multivalent binding of formin-binding protein 21 (FBP21)-tandem-WW domains fosters protein recognition in the pre-spliceosome. The Journal of biological chemistry 27 21917930
2020 Cytosolic sequestration of the vitamin D receptor as a therapeutic option for vitamin D-induced hypercalcemia. Nature communications 26 33288743
2011 Borrelidin modulates the alternative splicing of VEGF in favour of anti-angiogenic isoforms. Chemical science 23 22822423
2017 A new role for FBP21 as regulator of Brr2 helicase activity. Nucleic acids research 20 28838205
2023 Bi-allelic loss-of-function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental syndrome. American journal of human genetics 15 37963460
2021 A novel 13 RNA binding proteins (RBPs) signature could predict prostate cancer biochemical recurrence. Pathology, research and practice 15 34419719
2021 BCL-2 Inhibitor ABT-737 Effectively Targets Leukemia-Initiating Cells with Differential Regulation of Relevant Genes Leading to Extended Survival in a NRAS/BCL-2 Mouse Model of High Risk-Myelodysplastic Syndrome. International journal of molecular sciences 15 34638998
2024 Cryo-EM analyses of dimerized spliceosomes provide new insights into the functions of B complex proteins. The EMBO journal 14 38383864
2024 The spectrum of pre-mRNA splicing in autism. Wiley interdisciplinary reviews. RNA 13 38509732
2017 Transcriptome analysis for UVB-induced phototoxicity in mouse retina. Environmental toxicology 13 29044990
2004 Identification and characterization of the human FMN1 gene in silico. International journal of molecular medicine 12 15202026
2004 Characterization of FMN2 gene at human chromosome 1q43. International journal of molecular medicine 12 15289902
2022 A multi-factor trafficking site on the spliceosome remodeling enzyme BRR2 recruits C9ORF78 to regulate alternative splicing. Nature communications 10 35241646
2015 Exploring monovalent and multivalent peptides for the inhibition of FBP21-tWW. Beilstein journal of organic chemistry 10 26124874
2014 Functional characterization of duplicated Suppressor of Overexpression of Constans 1-like genes in petunia. PloS one 9 24787903
2001 Role of nuclear WW domains and proline-rich proteins in dinoflagellate transcription. Protist 9 11545436
2015 Peptide-polymer ligands for a tandem WW-domain, an adaptive multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands. Beilstein journal of organic chemistry 8 26124884
2022 Target Recognition in Tandem WW Domains: Complex Structures for Parallel and Antiparallel Ligand Orientation in h-FBP21 Tandem WW. Journal of chemical information and modeling 5 35347992
2018 FBP21's C-Terminal Domain Remains Dynamic When Wrapped around the c-Sec63 Unit of Brr2 Helicase. Biophysical journal 2 30558886
2023 Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome. medRxiv : the preprint server for health sciences 1 37425688
2026 Regulatory Potential of piRNAs Targeting Klotho and Other Genes. Genes 0 41751625

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