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Showing FKBP3FKBP25 is a alias.

FKBP3

Peptidyl-prolyl cis-trans isomerase FKBP3 · UniProt Q00688

Length
224 aa
Mass
25.2 kDa
Annotated
2026-06-09
29 papers in source corpus 23 papers cited in narrative 24 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

FKBP3 (FKBP25) is a predominantly nuclear peptidylprolyl cis-trans isomerase that couples prolyl isomerase activity to nucleic-acid binding to act in ribosome biogenesis, chromatin regulation, genome maintenance, and the mitotic apparatus (PMID:1375932, PMID:26762975). It is a two-domain protein: a C-terminal FK506-binding/PPIase domain that hydrolyzes peptidyl-prolyl bonds, binds rapamycin with higher affinity than FK506, and is inhibited by both drugs (PMID:1375932); and an N-terminal Basic Tilted Helix Bundle (BTHB/HLH) domain that, together with a basic FKBD loop, makes major- and minor-groove contacts on DNA (PMID:24667607, PMID:26762975) and selectively binds double-stranded RNA — an activity that drives its nucleolar localization and the bulk of its protein interactions, including with nucleolin and the immature pre-60S ribosomal subunit (PMID:24840943, PMID:29036638). The catalytic PPIase activity is required for homologous-recombination repair of DNA double-strand breaks, with FKBP3-depleted cells forming fewer Rad51 foci and shifting toward Rad52-dependent single-strand annealing (PMID:30620620). The FKBD domain directly binds and stabilizes microtubules, and FKBP3 associates with the mitotic spindle and safeguards chromosome stability, with its chromatin association switched off during mitosis by PKC-mediated phosphorylation (PMID:29361176). FKBP3 also operates as a chromatin regulator and proliferation driver: it stabilizes Sp1 to upregulate HDAC2 and repress p27 (PMID:28839465), and binds the transcription factor YY1 to recruit HDAC1/2 to target promoters, a mechanism it uses to enforce HIV-1 latency at the viral LTR (PMID:34281390). It additionally tunes the p53 axis by stimulating MDM2 auto-ubiquitylation and degradation (PMID:19166840) and, via ESD-mediated suppression of K48-linked ubiquitination that stabilizes the cytoplasmic pool, suppresses mTORC1 activity to promote autophagy (PMID:34875997). FKBP3 forms a rapamycin-induced ternary complex with the FRB domain of mTOR, defined at atomic resolution (PMID:27610411).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 1992 High

    Established that FKBP3 is an enzymatically active prolyl isomerase distinct from FKBP12, defining its core catalytic identity and drug sensitivity.

    Evidence In vitro PPIase assays with recombinant protein and rapamycin/FK506 inhibition; cDNA cloning revealing nuclear localization sequences

    PMID:1375932

    Open questions at the time
    • Physiological substrates of the PPIase activity not identified
    • Nuclear targeting predicted from sequence, not functionally tested at this stage
  2. 1993 Medium

    Showed that FKBP3 is nuclear and binds DNA, a property absent in homologous FKBP12, pointing to a chromatin-associated function beyond isomerase activity.

    Evidence Cell fractionation and DNA-binding assays in Jurkat cells with FKBP12 negative control

    PMID:8422914

    Open questions at the time
    • DNA sequence specificity not defined
    • Domain responsible for DNA binding not mapped
  3. 1999 Medium

    Placed FKBP3 downstream of the p53 stress response by identifying it as a transcriptionally repressed p53 target during DNA damage.

    Evidence Differential expression screening after p53 induction across multiple cell lines and damaging stimuli

    PMID:10557083

    Open questions at the time
    • Mechanism of p53-mediated repression not dissected
    • Functional consequence of downregulation not established here
  4. 2009 Medium

    Defined a feedback link to p53 by showing FKBP3 stimulates MDM2 auto-ubiquitylation, thereby raising p53 and p21.

    Evidence Co-IP plus siRNA knockdown with MDM2/p53/p21 western readouts

    PMID:19166840

    Open questions at the time
    • Whether PPIase activity is required not tested
    • Single lab, no reciprocal/structural validation of FKBP3-MDM2 contact
  5. 2014 Medium

    Connected FKBP3 to ribosome biogenesis and solved the N-terminal domain fold, establishing a structural basis for its nucleic-acid engagement.

    Evidence MS of immunoprecipitates with RNase-sensitivity tests showing nucleolin/pre-60S association; NMR structure of FKBP25(1-73) defining the BTHB fold

    PMID:24667607 PMID:24840943

    Open questions at the time
    • Direct catalytic role in ribosome assembly not shown
    • BTHB nucleic-acid selectivity not yet resolved at this stage
  6. 2016 High

    Provided full-length and complex structures showing inter-domain communication, dual-groove DNA binding, and the rapamycin-bridged FKBP3-mTOR(FRB) ternary complex.

    Evidence NMR of full-length FKBP25 with DNA titration and mutagenesis; X-ray crystallography of FRB-rapamycin-FKBP25 at 1.67 Å

    PMID:26762975 PMID:27610411

    Open questions at the time
    • In vivo significance of the mTOR ternary complex not established
    • Whether DNA binding and PPIase act simultaneously unclear
  7. 2017 High

    Resolved the molecular logic of FKBP3 localization by showing the BTHB domain selectively binds dsRNA, which drives nucleolar targeting and most of its interactome.

    Evidence dsRNA-binding assays, mutagenesis, immunofluorescence, and Co-IP in BTHB mutants

    PMID:29036638

    Open questions at the time
    • Specific dsRNA targets in cells not identified
    • Relationship between dsRNA and DNA binding modes not reconciled
  8. 2017 Medium

    Defined a proliferation-driving chromatin axis whereby FKBP3 stabilizes Sp1 to upregulate HDAC2 and repress p27.

    Evidence siRNA/overexpression, Sp1 ubiquitination assay, HDAC2-p27 promoter ChIP, and proliferation assays in NSCLC models

    PMID:28839465

    Open questions at the time
    • Whether PPIase activity drives Sp1 stabilization not tested
    • Direct enzyme-substrate relationship with Sp1 not shown
  9. 2018 High

    Established a structural role at the mitotic apparatus, showing the FKBD domain directly stabilizes microtubules and that cell-cycle PKC phosphorylation toggles chromatin versus spindle engagement.

    Evidence In vitro microtubule-binding assay, mitotic spindle immunofluorescence, chromosome instability assays, and PKC phosphorylation assays

    PMID:29361176

    Open questions at the time
    • PKC site(s) and kinase specificity in vivo not fully mapped
    • How spindle and DNA-repair roles are temporally coordinated unclear
  10. 2019 High

    Demonstrated that the catalytic PPIase activity is required for homologous-recombination repair, assigning an enzymatic function to genome maintenance.

    Evidence Catalytic-mutant rescue, Rad51/Rad52 focus assays, Rad52 epistasis, and DSB reporter assays

    PMID:30620620

    Open questions at the time
    • HR substrate isomerized by FKBP3 not identified
    • Rapamycin's mTOR-independent HR effect not fully delineated
  11. 2021 Medium

    Extended the YY1/HDAC repression mechanism to viral chromatin, showing FKBP3 enforces HIV-1 latency by recruiting HDAC1/2 to the LTR via YY1.

    Evidence CRISPR knockout in latent HIV models, FKBP3-YY1 Co-IP, and HDAC1/2 LTR ChIP

    PMID:34281390

    Open questions at the time
    • Whether DNA/PPIase activities contribute beyond YY1 bridging unclear
    • Generality to host gene promoters not defined
  12. 2021 Medium

    Identified an ESD-controlled stability switch that links FKBP3 abundance to mTORC1 suppression and autophagy.

    Evidence Yeast two-hybrid, Co-IP, K48-ubiquitination assay, and mTORC1/P70S6K/4EBP1 phospho-readouts

    PMID:34875997

    Open questions at the time
    • Identity of the E3 ligase opposed by ESD unknown
    • Relationship to the rapamycin-induced FRB ternary complex not integrated
  13. 2021 Medium

    Confirmed an in vivo meiotic requirement, with FKBP3 needed for proper spindle assembly and kinetochore-microtubule attachment in oocytes.

    Evidence siRNA knockdown in mouse oocytes, spindle/chromosome immunofluorescence, aneuploidy scoring, and S163A mutagenesis

    PMID:33553183

    Open questions at the time
    • Mechanism linking S163 phosphorylation to function not resolved
    • Whether the microtubule-binding FKBD mediates this directly not shown

Open questions

Synthesis pass · forward-looking unresolved questions
  • The endogenous prolyl-isomerase substrates that underlie FKBP3's roles in HR repair, ribosome biogenesis, and chromatin regulation remain unidentified, leaving the unifying catalytic mechanism open.
  • No physiological PPIase substrate validated
  • How nucleic-acid binding, catalysis, and protein scaffolding are integrated into one mechanism is unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 3 GO:0016853 isomerase activity 3 GO:0003723 RNA binding 2 GO:0140110 transcription regulator activity 2 GO:0008092 cytoskeletal protein binding 1
Localization
GO:0005634 nucleus 2 GO:0005730 nucleolus 1 GO:0005829 cytosol 1
Pathway
R-HSA-162582 Signal Transduction 2 R-HSA-1640170 Cell Cycle 2 R-HSA-4839726 Chromatin organization 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-73894 DNA Repair 1
Complex memberships
FKBP25-rapamycin-mTOR(FRB) ternary complexpre-60S ribosomal subunit

Evidence

Reading pass · 24 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1992 FKBP25 (FKBP3) has peptidylprolyl cis-trans isomerase (PPIase) activity comparable to FKBP12, binds rapamycin with higher affinity than FK506 (IC50 ~50 nM vs ~400 nM), and its PPIase activity is inhibited by rapamycin and FK506. In vitro PPIase assay with recombinant FKBP25; inhibition assays with rapamycin and FK506 The Journal of biological chemistry High 1375932
1992 FKBP25 contains putative nuclear localization sequences in its sequence, distinguishing it from FKBP12 and FKBP13. cDNA cloning and sequence analysis The Journal of biological chemistry Medium 1375932
1993 FKBP25 is predominantly localized to the nuclear fraction of T-lymphoma Jurkat cells and has the ability to bind DNA; the FKBP25/DNA complex is dissociable by high salt. FKBP12, which shares C-terminal homology with FKBP25, does not bind DNA. Cell fractionation, Western blotting with anti-FKBP25 antibodies, DNA-binding assay FEBS letters Medium 8422914
1999 FKBP25 (FKBP3) expression is down-regulated following p53 induction by DNA-damaging stimuli in human and murine cell lines, identifying it as a transcriptional repression target of p53. Differential gene expression screening following p53 induction; confirmed in multiple cell lines with DNA-damaging stimuli Oncogene Medium 10557083
2000 Endogenous FKBP25 from porcine brain co-isolates with high-mobility group II protein (HMG-II), and a residual pool associates with Rab5, guanylyl kinase, and phosphatidylethanolamine-binding protein. Immunoblotting, 2D-PAGE, Edman degradation, MALDI-TOF of anti-FKBP25 immunoprecipitates from porcine brain Archives of biochemistry and biophysics Low 10900128
2009 FKBP25 interacts with MDM2, stimulates MDM2 auto-ubiquitylation and proteasomal degradation, leading to induction of p53 and p21. Depletion of FKBP25 by siRNA increases MDM2 levels and reduces p53 and p21. Co-immunoprecipitation, siRNA knockdown, western blotting for MDM2/p53/p21 levels FEBS letters Medium 19166840
2013 Mutagenesis of FKBP25 revealed that certain mutations destabilize the FKBD domain fold entirely, while other 'surgical' mutations specifically ablate PPIase catalytic activity while maintaining domain structure, enabling distinction between catalytic and non-catalytic functions. Site-directed mutagenesis, in vitro PPIase assays, structural characterization of mutants Biochemical Society transactions Medium 23697935
2014 FKBP25 interacts with nucleolin in an rRNA-dependent manner and associates with the immature pre-60S ribosomal subunit in nuclear extract but not with mature ribosomes, implicating FKBP25 in ribosome biogenesis. Proteomic characterization (mass spectrometry of immunoprecipitates), Co-IP with RNase treatment to assess rRNA-dependence RNA (New York, N.Y.) Medium 24840943
2014 The N-terminal domain of FKBP25 (residues 1–73) adopts a novel 5-helix bundle structure termed the Basic Tilted Helix Bundle (BTHB) with a positively charged surface patch, which is implicated in DNA binding. NMR/structural determination of FKBP25(1-73), comparative structural analysis with HectD1 Biochemical and biophysical research communications Medium 24667607
2014 Endogenous FKBP25 associates with core histones, spliceosomal complexes, ribosomal subunits, and polyribosomes; FKBP25 from polyribosomes can be released by added RNA or high salt, indicating RNA-mediated interaction. Rapamycin or FK506 only partially release FKBP25, suggesting additional protein-mediated binding via the PPIase cavity. Anti-FKBP25 immunoprecipitation from HeLa, K568, and porcine brain cells; polyribosome fractionation; salt/RNA competition; proteomics Biochemical and biophysical research communications Low 24998444
2015 FKBP25 associates with TRPC6 (and TRPC3), and its interaction pattern with TRPCs is modified by FK506. Knockdown of FKBP25 significantly inhibits OAG-evoked non-capacitative calcium entry (NCCE) in MEG-01 and HEK293 cells. Biotinylation experiments indicate FKBP25 localizes to the plasma membrane in addition to intracellular compartments. Co-immunoprecipitation, siRNA knockdown, calcium entry assays, surface biotinylation in platelets and cell lines Biochimica et biophysica acta Medium 26239116
2016 FKBP25 forms a rapamycin-induced ternary complex with the FRB domain of mTOR, and the crystal structure of FRB-rapamycin-FKBP25 was determined at 1.67-Å resolution, revealing conformational changes in FRB and covalent metalloid coordination at C2085 of FRB. Proximity biotin labeling (pBirA), immunoprecipitation, immunofluorescence, X-ray crystallography ACS central science High 27610411
2016 NMR solution structure of full-length human FKBP25 shows the N-terminal HLH domain and C-terminal FKBD interact with each other; both domains participate in DNA binding, with the HLH domain making major-groove contacts and a basic FKBD loop contributing to minor-groove interactions. NMR structure determination, NMR-monitored DNA titration, mutagenesis, FKBP25-DNA complex modeling Nucleic acids research High 26762975
2017 The N-terminal BTHB domain of FKBP25 selectively binds double-stranded RNA (dsRNA) over DNA or single-stranded oligonucleotides. This RNA-binding activity is required for FKBP25's nucleolar localization and for the vast majority of its protein interactions, including those with pre-60S ribosomes and early ribosome biogenesis factors. Biochemical dsRNA-binding assays, mutagenesis, immunofluorescence for localization, Co-IP for protein interactions in BTHB mutants Nucleic acids research High 29036638
2017 FKBP3 promotes NSCLC cell proliferation via a pathway in which FKBP3 inhibits ubiquitination of Sp1, stabilizing Sp1, which drives HDAC2 promoter activity, increasing HDAC2 expression, leading to HDAC2-mediated deacetylation of histone H3K4 at the p27 promoter and reduced p27 expression. siRNA knockdown, overexpression, ChIP (HDAC2 at p27 promoter), ubiquitination assay for Sp1, western blotting, in vitro and in vivo proliferation assays Theranostics Medium 28839465
2018 The FKBP domain of FKBP25 directly binds microtubules in vitro to promote their polymerization and stabilize the MT network. FKBP25 associates with the mitotic spindle, regulates entry into mitosis, and its knockdown leads to increased chromosome instability. Additionally, FKBP25 association with chromatin is regulated by Protein Kinase C (PKC) phosphorylation in a cell-cycle-dependent manner, disrupting FKBP25-DNA contacts during mitosis while maintaining spindle association. Direct microtubule-binding assay (in vitro), mitotic spindle immunofluorescence, chromosome instability assays in FKBP25 knockdown cells, PKC phosphorylation assays Nucleic acids research High 29361176
2018 FKBP25 translocates from cytoplasm to nucleus in endothelial cells following oxygen-glucose deprivation (OGD) or peroxynitrite treatment, and in the nucleus interacts with 60S ribosomal protein L7a. Overexpression of FKBP25 protects endothelial cells against OGD injury. Western blot and immunofluorescence (localization), co-immunoprecipitation and FRET (interaction with L7a), overexpression survival assay Cellular physiology and biochemistry Medium 29969783
2019 FKBP25's catalytic (PPIase) activity is required for promoting homologous recombination (HR) repair of DNA double-strand breaks (DSBs). FKBP25-depleted cells form fewer Rad51 repair foci and become dependent on Rad52-mediated single-strand annealing (SSA). Rapamycin treatment also impairs HR, at least partly independently of mTOR. FKBP25 knockdown, catalytic mutant expression, Rad51/Rad52 focus assays (immunofluorescence), genetic epistasis (Rad52 dependence), DSB reporter assays Biochemistry and cell biology High 30620620
2019 FKBP3 downregulation in colorectal cancer cells reduces HDAC2 expression and P-gp levels, reduces p-AKT, and increases PTEN and cleaved caspase-3, sensitizing cells to oxaliplatin. Upregulation of HDAC2 counteracts FKBP3 knockdown-induced sensitization. siRNA knockdown and overexpression, western blotting, flow cytometry (apoptosis), rescue by HDAC2 overexpression Oncology reports Medium 31524278
2021 FKBP3 indirectly binds the HIV-1 LTR through physical interaction with the transcription factor YY1, thereby recruiting HDAC1/2 to the LTR, promoting histone deacetylation and HIV-1 latency. FKBP3 knockout in latently infected cells activates latent HIV-1. CRISPR knockout in latent HIV-1 cell lines, Co-IP (FKBP3-YY1 interaction), ChIP (HDAC1/2 at LTR), primary latent cell model mBio Medium 34281390
2021 Esterase D (ESD) interacts with FKBP25 via the N-terminal 1–90 aa domain of FKBP25. ESD reduces K48-linked poly-ubiquitin chains on FKBP25, thereby stabilizing cytoplasmic FKBP25. Stabilized FKBP25 then binds more mTORC1, suppressing mTORC1 activity and promoting autophagy. Yeast two-hybrid, Co-IP (endogenous and GFP-tagged FKBP25), ubiquitination assay, western blot for mTORC1/P70S6K/4EBP1 phosphorylation Cellular & molecular biology letters Medium 34875997
2021 FKBP25 depletion in mouse oocytes causes abnormal spindle assembly, chromosome misalignment, and defective kinetochore-microtubule attachment, leading to elevated aneuploidy. Phosphorylation at serine 163 is identified as a key regulatory modification for FKBP25's function in meiotic maturation. siRNA knockdown in mouse oocytes, immunofluorescence (spindle/chromosome), aneuploidy scoring, site-directed mutagenesis (S163A) Frontiers in cell and developmental biology Medium 33553183
2023 FKBP3 interacts with PARK7 (DJ-1); knockdown of FKBP3 enhances ubiquitination and degradation of PARK7, reducing Wnt/β-catenin pathway activation in DLBCL cells. Co-immunoprecipitation (FKBP3-PARK7 interaction), ubiquitination assay, western blotting for β-catenin pathway components, FKBP3 knockdown Journal of cellular and molecular medicine Low 37987202
2023 FKBP25 knockdown in C2C12 myoblasts increases cell accumulation/viability and migration in vitro, independently of changes in tubulin dynamics. FKBP25 protein expression increases in hypertrophy (chronic mechanical overload) and muscle regeneration (mdx model) but decreases in denervation atrophy in vivo. Doxycycline-inducible knockdown in C2C12 cells, viability and migration assays, tubulin dynamics measurements, in vivo muscle adaptation models with western blotting The FEBS journal Low 37345229

Source papers

Stage 0 corpus · 29 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1999 Down-regulation of the stathmin/Op18 and FKBP25 genes following p53 induction. Oncogene 110 10557083
1992 Molecular cloning of a 25-kDa high affinity rapamycin binding protein, FKBP25. The Journal of biological chemistry 77 1375932
2009 FKBP25, a novel regulator of the p53 pathway, induces the degradation of MDM2 and activation of p53. FEBS letters 58 19166840
2017 FKBP3 Promotes Proliferation of Non-Small Cell Lung Cancer Cells through Regulating Sp1/HDAC2/p27. Theranostics 54 28839465
2016 Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells. ACS central science 47 27610411
1993 On the localization of FKBP25 in T-lymphocytes. FEBS letters 43 8422914
2019 Melatonin Regulates Breast Cancer Progression by the lnc010561/miR-30/FKBP3 Axis. Molecular therapy. Nucleic acids 32 31955008
2019 FKBP3 mediates oxaliplatin resistance in colorectal cancer cells by regulating HDAC2 expression. Oncology reports 29 31524278
2016 Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin. Nucleic acids research 26 26762975
2014 The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit. RNA (New York, N.Y.) 24 24840943
2018 The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability. Nucleic acids research 18 29361176
2017 The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module. Nucleic acids research 14 29036638
2014 Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities. Biochemical and biophysical research communications 14 24998444
2014 Basic Tilted Helix Bundle - a new protein fold in human FKBP25/FKBP3 and HectD1. Biochemical and biophysical research communications 13 24667607
2000 Mammalian FKBP-25 and its associated proteins. Archives of biochemistry and biophysics 13 10900128
2013 Resolving the functions of peptidylprolyl isomerases: insights from the mutagenesis of the nuclear FKBP25 enzyme. Biochemical Society transactions 12 23697935
1996 Cloning and high expression of rabbit FKBP25 in cornea. Japanese journal of ophthalmology 10 8876379
2021 Esterase D stabilizes FKBP25 to suppress mTORC1. Cellular & molecular biology letters 9 34875997
2015 FKBP25 and FKBP38 regulate non-capacitative calcium entry through TRPC6. Biochimica et biophysica acta 9 26239116
2019 FKBP25 participates in DNA double-strand break repair. Biochemistry and cell biology = Biochimie et biologie cellulaire 8 30620620
2021 FKBP3 Induces Human Immunodeficiency Virus Type 1 Latency by Recruiting Histone Deacetylase 1/2 to the Viral Long Terminal Repeat. mBio 7 34281390
2023 Knockdown of FKBP3 suppresses nasopharyngeal carcinoma cell growth, invasion and migration, deactivated NF-κB/IL-6 signaling pathway through inhibiting histone deacetylase 2 expression. The Chinese journal of physiology 6 37082996
2018 Elucidation of the FKBP25-60S Ribosomal Protein L7a Stress Response Signaling During Ischemic Injury. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 6 29969783
2005 Molecular cloning and expression pattern of the Fkbp25 gene during cerebral cortical neurogenesis. Gene expression patterns : GEP 6 15908283
2023 FKBP3 aggravates the malignant phenotype of diffuse large B-cell lymphoma by PARK7-mediated activation of Wnt/β-catenin signalling. Journal of cellular and molecular medicine 5 37987202
2002 Cloning and identification of a novel cDNA which may be associated with FKBP25. Biochemical genetics 5 12392168
2021 FKBP25 Regulates Meiotic Apparatus During Mouse Oocyte Maturation. Frontiers in cell and developmental biology 4 33553183
2023 FKBP25 regulates myoblast viability and migration and is differentially expressed in in vivo models of muscle adaptation. The FEBS journal 1 37345229
2023 [Procine recombinant NK-lysin inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 and inhibiting oxidative phosphorylation and glycolysis: a proteomic analysis]. Nan fang yi ke da xue xue bao = Journal of Southern Medical University 0 37488794

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