Affinage

RAB5B

Ras-related protein Rab-5B · UniProt P61020

Length
215 aa
Mass
23.7 kDa
Annotated
2026-06-10
24 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RAB5B is a small Rab GTPase that controls early endosomal membrane fusion and endocytic trafficking, binding GTP and GDP with low intrinsic hydrolysis activity and localizing to the plasma membrane (PMID:1541686). In its GTP-bound state it directly recruits the early endosomal tethering factor EEA1, with which it colocalizes on early endosomes, providing the molecular basis for endosome fusion (PMID:10491193). RAB5B activity is regulated by phosphorylation: LRRK2 phosphorylates Thr6, enhancing GTPase activity and producing inactive-RAB5B phenotypes including reduced EGFR degradation, while cdc2 kinase phosphorylates Ser-123 (PMID:25605758, PMID:10403367). Through this endocytic and fusion machinery RAB5B supports diverse cargo-handling pathways — it facilitates NMDA receptor endocytosis underlying neuroprotection (PMID:15518642) and is required for trafficking and maturation of pulmonary surfactant proteins, where a dominant-negative p.Asp136His variant disrupts early endosome fusion and blocks processing of proSP-B and proSP-C (PMID:35121658). Beyond these core roles, RAB5B participates in trafficking events co-opted in disease contexts, including ER-to-multivesicular-body transport of the hepatitis B large surface protein (PMID:31118260).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 1992 Medium

    Established RAB5B as a bona fide small GTPase with nucleotide-binding and slow hydrolysis kinetics, defining its biochemical identity and membrane association.

    Evidence GST fusion purification, GTP/GDP binding and hydrolysis assays, immunofluorescence and subcellular fractionation

    PMID:1541686

    Open questions at the time
    • No effector or regulator identified at this stage
    • Plasma membrane localization not yet reconciled with endosomal function
  2. 1999 High

    Identified EEA1 as a GTP-dependent direct effector, providing the mechanistic link between RAB5B activation and early endosomal tethering/fusion.

    Evidence Yeast two-hybrid screen with biochemical binding confirmation, confocal colocalization, and GAP/GTPase activity assays on brain cytosol

    PMID:10491193

    Open questions at the time
    • The brain GAP activity stimulating RAB5B was not molecularly identified
    • Functional consequence of EEA1 binding for fusion not directly tested here
  3. 1999 Medium

    Showed RAB5 isoforms are differentially phosphorylated, with cdc2 targeting RAB5B Ser-123, raising the possibility of cell-cycle-coupled regulation distinct from other isoforms.

    Evidence In vitro kinase assays with recombinant RAB5 isoforms and purified ERK1/ERK2/cdc2

    PMID:10403367

    Open questions at the time
    • In vitro only; cellular phosphorylation not demonstrated
    • Functional effect of Ser-123 phosphorylation unknown
  4. 2004 Medium

    Placed RAB5B functionally in a neuronal endocytic pathway by showing it is required for NMDA-receptor-endocytosis-dependent neuroprotection.

    Evidence Antisense knockdown in organotypic hippocampal cultures with viability readout and pharmacological endocytosis blockade

    PMID:15518642

    Open questions at the time
    • Direct demonstration that RAB5B drives NMDA receptor internalization not shown
    • Effectors mediating this neuronal role unidentified
  5. 2015 High

    Defined LRRK2 as a kinase regulator of RAB5B, with Thr6 phosphorylation enhancing GTPase activity to negatively tune RAB5B signaling.

    Evidence In vitro kinase assay with MS site mapping, cellular validation with LRRK2 G2019S, neurite outgrowth, EGFR degradation, and GTPase assays

    PMID:25605758

    Open questions at the time
    • Whether LRRK2 acts directly as a GAP or via another mechanism not resolved
    • Physiological contexts of Thr6 phosphorylation in vivo not established
  6. 2018 Medium

    Linked RAB5B to cancer cell behavior as a miR-130a-3p target whose depletion impairs proliferation, migration, and invasion.

    Evidence miRNA over/knockdown and RAB5B siRNA with proliferation/migration/invasion assays in breast cancer stem-like cells

    PMID:29746865

    Open questions at the time
    • Direct miRNA-RAB5B binding not validated
    • Trafficking mechanism connecting RAB5B to invasive phenotype not defined
  7. 2019 Medium

    Demonstrated a required role for RAB5B in ER-to-MVB transport, exploited by hepatitis B large surface protein, and an unexpected effect on viral transcription.

    Evidence siRNA screen of 62 Rabs in HepG2.2.15 cells, northern blotting, immunofluorescence

    PMID:31118260

    Open questions at the time
    • Mechanism linking RAB5B loss to HNF4α/LHBs transcription unclear
    • Effectors mediating ER-to-MVB transport unidentified
  8. 2022 High

    Connected RAB5B-dependent endosome fusion to surfactant protein maturation and established a dominant-negative disease variant impairing endocytosis.

    Evidence C. elegans ortholog knock-in of p.Asp136His, endocytosis and early endosome fusion assays, patient lung immunostaining and colocalization

    PMID:35121658

    Open questions at the time
    • Direct biochemical effect of D136H on nucleotide cycling not shown
    • Whether proSP processing failure is due to endosomal or upstream routing not fully dissected
  9. 2023 Low

    Implicated RAB5B in endocytic melanocore clustering downstream of tranexamic acid in keratinocytes.

    Evidence Transcriptome sequencing, siRNA silencing, TEM, colocalization with LAMP1

    PMID:36779692

    Open questions at the time
    • Single lab with limited mechanistic follow-up
    • Effectors and trafficking steps for melanocore clustering undefined
  10. 2024 Low

    Reported a non-canonical RAB5B function via CD109 interaction at MVB lipid rafts to package circRNA into extracellular vesicles in pancreatic cancer.

    Evidence Co-IP, lipid raft fractionation, EV isolation, in vitro and in vivo assays

    PMID:39488792

    Open questions at the time
    • Single Co-IP without reciprocal validation
    • Mechanism of lipid raft anchoring inferred from limited fractionation data
  11. 2025 Low

    Proposed RAB5B-positive endosomes as carriers delivering the LC3 lipidation complex to synapses under nutrient stress, coupling endosomal trafficking to localized autophagy.

    Evidence Live imaging, co-trafficking analysis, dynein inhibition, autophagy assays, synaptic proteomics (preprint)

    PMID:bio_10.1101_2025.11.25.690410

    Open questions at the time
    • Preprint, not peer-reviewed
    • Direct interaction between RAB5B and ATG16L1/ATG5 not demonstrated
    • Mechanism of nutrient-stress-triggered recruitment unclear

Open questions

Synthesis pass · forward-looking unresolved questions
  • The full set of RAB5B GEFs and GAPs and the structural basis for its functional differences from RAB5A/RAB5C remain undefined.
  • No GEF identified for RAB5B
  • GAP stimulating RAB5B not molecularly characterized
  • No structural model linking nucleotide state to effector selectivity

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003924 GTPase activity 3
Localization
GO:0005768 endosome 2 GO:0005886 plasma membrane 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-9612973 Autophagy 1
Partners
CD109EEA1LRRK2

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1992 RAB5B was identified as a 215-amino-acid small GTPase that binds GTP and GDP, displays low intrinsic GTP hydrolysis activity (~0.005/min), and localizes to the plasma membrane by subcellular fractionation and indirect immunofluorescence. GST fusion protein purification, GTP/GDP binding assay, GTP hydrolysis assay, indirect immunofluorescence, subcellular fractionation The Journal of Clinical Investigation Medium 1541686
1999 EEA1 (early endosomal autoantigen) directly interacts with RAB5B in a GTP-dependent manner via both its C-terminal and N-terminal domains, and EEA1 colocalizes with RAB5B on early endosomes. A pig brain cytosol GAP activity preferentially stimulates RAB5B GTPase activity over RAB5A. Yeast two-hybrid screen, biochemical binding confirmation, confocal immunofluorescence, GTPase activity assay European Journal of Biochemistry High 10491193
1999 The three RAB5 isoforms (RAB5A, RAB5B, RAB5C) are differentially phosphorylated in vitro: RAB5A is efficiently phosphorylated by ERK1 but not ERK2, while cdc2 kinase preferentially phosphorylates Ser-123 of RAB5B. In vitro kinase assay with recombinant proteins and purified kinases (ERK1, ERK2, cdc2) FEBS Letters Medium 10403367
2004 RAB5B is required for DHPG-mediated neuroprotection against NMDA toxicity in organotypic hippocampal cultures; antisense oligonucleotide knockdown of RAB5B suppressed DHPG-induced protection, and this protection was abolished by disrupting endocytosis via osmotic shock/K+ depletion, placing RAB5B in a pathway facilitating NMDA receptor endocytosis. Antisense oligonucleotide knockdown in organotypic hippocampal cultures, cell viability assay, pharmacological inhibition of endocytosis Brain Research Medium 15518642
2015 LRRK2 kinase phosphorylates RAB5B at Thr6 in vitro and in cells expressing LRRK2 G2019S. Phosphomimetic T6D mutation enhances RAB5B GTPase activity and produces phenotypes consistent with inactive RAB5B (longer neurite length, reduced EGFR degradation), suggesting LRRK2 acts as a GAP-like regulator of RAB5B signaling. In vitro kinase assay with recombinant proteins, mass spectrometry, western blot with phospho-specific approach, neurite outgrowth assay, EGFR degradation assay, GTPase activity assay Journal of Biochemistry High 25605758
2019 RAB5B knockdown increases HBV DNA production >30-fold by increasing LHBs mRNA transcription (via HNF4α upregulation) and is required for transport of large hepatitis B surface protein (LHBs) from the ER to multivesicular bodies (MVB); depletion causes LHBs accumulation in the ER. siRNA knockdown in HepG2.2.15 cells, northern blotting, immunofluorescence microscopy, siRNA screen of 62 Rab proteins Journal of Virology Medium 31118260
2018 RAB5B is a direct target of miR-130a-3p; overexpression of miR-130a-3p downregulates RAB5B protein and knockdown of RAB5B inhibits proliferation, migration, and invasion of breast cancer stem cell-like cells. miRNA overexpression/knockdown, RAB5B siRNA knockdown, proliferation/migration/invasion assays Biochemical and Biophysical Research Communications Medium 29746865
2022 A dominant negative RAB5B variant (p.Asp136His) causes defective early endosome (EE) fusion and endocytosis, leading to failure to process proSP-B and proSP-C into mature surfactant proteins SP-B and SP-C in alveolar type II cells. RAB5B and EEA1 colocalize with proSP-B and proSP-C in normal lung, establishing RAB5B and early endosomes as required for the surfactant protein trafficking/processing pathway. Knock-in of variant into C. elegans ortholog (genetic epistasis), endocytosis assays, early endosome fusion assay, immunostaining of patient lung biopsy, colocalization microscopy Proceedings of the National Academy of Sciences of the United States of America High 35121658
2023 RAB5B is upregulated by tranexamic acid (TXA) in keratinocytes and promotes clustering of endocytic melanocores; RAB5B silencing reduces melanocore clustering, and melanocores colocalize with RAB5B and LAMP1. Transcriptome sequencing, RAB5B siRNA silencing, transmission electron microscopy, colocalization microscopy Experimental Dermatology Low 36779692
2024 RAB5B interacts with CD109 in KRAS-mutant pancreatic cancer cells; this interaction bypasses canonical endosomal trafficking by anchoring RAB5B to lipid rafts of multivesicular bodies, facilitating packaging of circPNIT into CD109+ extracellular vesicles. Co-immunoprecipitation, lipid raft fractionation, extracellular vesicle isolation and analysis, in vitro and in vivo functional assays Advanced Science Low 39488792
2025 Under nutrient stress (serum withdrawal), the LC3 lipidation complex (ATG5–ATG12–ATG16L1) is recruited to synapses via RAB5B-positive endosomes in a dynein-dependent manner, coupling nutrient sensing to localized synaptic autophagy. Live imaging shows enhanced RAB5B–ATG16L1 co-trafficking and increased ATG5 mobility upon serum withdrawal. Live imaging, co-trafficking analysis, dynein inhibition, autophagy assays, synaptic proteomics bioRxiv (preprint)preprint Low bio_10.1101_2025.11.25.690410

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2018 MiR-130a-3p inhibits migration and invasion by regulating RAB5B in human breast cancer stem cell-like cells. Biochemical and biophysical research communications 89 29746865
1999 The small GTPases Rab5a, Rab5b and Rab5c are differentially phosphorylated in vitro. FEBS letters 72 10403367
2015 An early endosome regulator, Rab5b, is an LRRK2 kinase substrate. Journal of biochemistry 61 25605758
1999 Direct interaction of EEA1 with Rab5b. European journal of biochemistry 52 10491193
1992 Identification and subcellular localization of human rab5b, a new member of the ras-related superfamily of GTPases. The Journal of clinical investigation 40 1541686
2022 A dominant negative variant of RAB5B disrupts maturation of surfactant protein B and surfactant protein C. Proceedings of the National Academy of Sciences of the United States of America 30 35121658
2019 Small Interfering RNA Screening for the Small GTPase Rab Proteins Identifies Rab5B as a Major Regulator of Hepatitis B Virus Production. Journal of virology 26 31118260
2014 Plasmodium falciparum Rab5B is an N-terminally myristoylated Rab GTPase that is targeted to the parasite's plasma and food vacuole membranes. PloS one 26 24498355
2022 Loci on chromosome 12q13.2 encompassing ERBB3, PA2G4 and RAB5B are associated with polycystic ovary syndrome. Gene 17 36423778
2004 Antisense oligonucleotide against GTPase Rab5b inhibits metabotropic agonist DHPG-induced neuroprotection. Brain research 17 15518642
2020 Long non-coding RNA MIAT promotes gastric cancer proliferation and metastasis via modulating the miR-331-3p/RAB5B pathway. Oncology letters 13 33154765
2016 Plasmodium Rab5b is secreted to the cytoplasmic face of the tubovesicular network in infected red blood cells together with N-acylated adenylate kinase 2. Malaria journal 12 27316546
2015 Molecular cloning, characterization, and expression of Rab5B, Rab6A, and Rab7 from Litopenaeus vannamei (Penaeidae). Genetics and molecular research : GMR 12 26214455
2024 Role of Rabenosyn-5 and Rab5b in host cell cytosol uptake reveals conservation of endosomal transport in malaria parasites. PLoS biology 11 38820535
2023 hsa_circRNA_BECN1 acts as a ceRNA to promote polycystic ovary syndrome progression by sponging the miR-619-5p/Rab5b axis. Molecular human reproduction 10 37882757
2019 Association of single nucleotide polymorphisms in the RAB5B gene 3'UTR region with polycystic ovary syndrome in Chinese Han women. Bioscience reports 10 31036605
2021 Rab5b-Associated Arf1 GTPase Regulates Export of N-Myristoylated Adenylate Kinase 2 From the Endoplasmic Reticulum in Plasmodium falciparum. Frontiers in cellular and infection microbiology 7 33604307
2020 Rab5b function is essential to acquire heme from hemoglobin endocytosis for survival of Leishmania. Biochimica et biophysica acta. Molecular cell research 7 33011192
2006 Rab5b localization to early endosomes in the protozoan human pathogen Leishmania donovani. Molecular and cellular biochemistry 7 16752082
2024 Endosomal Trafficking Bypassed by the RAB5B-CD109 Interplay Promotes Axonogenesis in KRAS-Mutant Pancreatic Cancer. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 6 39488792
2023 Prediction of Rab5B inhibitors through integrative in silico techniques. Molecular diversity 6 37505376
2023 Tranexamic acid may promote melanocores clustering in keratinocytes through upregulation of Rab5b. Experimental dermatology 5 36779692
2026 Role of Rab5b in the defense of Cynoglossus semilaevis against Vibrio vulnificus infection. International journal of biological macromolecules 0 41831502
2026 Analysis of structure and stability of Leishmania donovani Rab5a and Rab5b. International journal of biological macromolecules 0 42070609

Missed literature

Know a paper Affinage missed for RAB5B? Flag it for the maintainers and the community.

No submissions yet.