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A novel homogenous polysaccharide LPWF together with its three acid hydrolysis products LPWF1–3 were isolated and prepared from lotus plumule (germs of Nelumbo nucifera). LPWF was composed of rhamnose (Rha), arabinose (Ara), galactose (Gal), xylose (Xyl), and galacturonic acid (GalA) in the molar ratio of 7.3: 34.0: 7.0: 19.1: 32.6 with a molecular weight of 567.6 kDa. The structure of LPWF was elucidated by methylation and NMR analysis of LPWF1–3 and a follow-up structural assembling aided by high-resolution mass spectrometry mapping of oligosaccharides and ROSEY spectra. LPWF was characterized as an unusual pectin linked by rhamnogalacturonan I (RGI, composed of LPWF1–2) and xylogalacturonan (XGA, LPWF3). LPWF1 was an arabinan peeled from the RGI part with a 1,5-linked backbone branching on the O -2 position, while LPWF2 was the remaining part of RGI composed of Rha (36.1%), Gal (17.8%), and GalA (43.7%). LPWF3 was identified as the XGA part with a backbone of α-1,4-linked GalA and branches of mono-xylose substitutions on the O -3 of GalA. LPWF (25 μg/mL) demonstrated significant inhibitions on the expression of IL-1β, IL-6, and TNF-α in LPS-stimulated primary murine microglia cultures. LPWF1 and 2 showed selectively and significantly inhibitory activity against the expression of IL-1β. • Structure features of the pectin LPWF was determined by NMR and methylation. • Structural characterization of LPWF was elucidated by assembling three stepwise hydrolyzed fragments. • LPWF is speculated to be a linearly linked RGI and XGA pectin. • The pectin LPWF could significantly inhibit the expression of IL-1β, IL-6, and TNF-α. [ABSTRACT FROM AUTHOR]