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Background Jujube (Ziziphus jujuba Mill.) fruit is one of the largest productions in China and its increasing production has drawn considerable attention from researchers. Polysaccharide is one of the most abundant components of jujube, and it represents a major group of biolotegically active constituents. This study intended to investigate the special structure of a homogeneous acidic polysaccharide (PZMP4) produced from Ziziphus Jujuba cv. Muzao fruit using novel methods, including DEAE-Sepharose Fast Flow and Sephacryl S-300 column chromatography. Results The structure of PZMP4 was determined via high-performance gel permeation chromatography (HPGPC), gas chromatography (GC), Fourier transform infrared spectroscopy (FT-IR), methylation analysis, nuclear magnetic resonance spectroscopy (NMR), scanning electron microscopy (SEM), and atomic force microscopy (AFM). The results reveal that PZMP4 with a molecular weight of 27.90 kDa was composed of rhamnose, arabinose, mannose, glucose, galactose, and galacturonic acid at a ratio of 2.32:2.21:0.22:0.88:2.08:8.83. Advanced structural analysis revealed a netted structure with molecular aggregates of PZMP4. Structural features demonstrated that the basic backbone of PZMP4 appeared to mainly consist of (1→4)-linked GalpA with three branches bonded to O-3 of (1→3)-linked Araf, (1→2)-linked Rhap, and terminated with GalpA. Conclusions PZMP4’s unique structure could imply distinct bioactivities and have considerable utilization in functional food. Graphic abstract

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