Honors & Awards

  • Alzheimer's Association Research Fellowship, Alzheimer's Association (2022-2025)

Professional Education

  • Doctor of Philosophy, Institute of Biophysics, Chinese Academy of Sciences, Biochemistry and Molecular Biology (2021)
  • Bachelor of Engineering, Jilin University, Bioengineering (2015)
  • Exchange student, Peking University, Biology (2013)

Stanford Advisors

All Publications

  • Structure and mechanism of the alkane-oxidizing enzyme AlkB. Nature communications Guo, X., Zhang, J., Han, L., Lee, J., Williams, S. C., Forsberg, A., Xu, Y., Austin, R. N., Feng, L. 2023; 14 (1): 2180


    Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms.

    View details for DOI 10.1038/s41467-023-37869-z

    View details for PubMedID 37069165

    View details for PubMedCentralID 4640736

  • Structure and thiazide inhibition mechanism of the human Na-Cl cotransporter. Nature Fan, M., Zhang, J., Lee, C. L., Zhang, J., Feng, L. 2023


    The sodium-chloride cotransporter (NCC) is critical for kidney physiology1. The NCC has a major role in salt reabsorption in the distal convoluted tubule of the nephron2,3, and mutations in the NCC cause the salt-wasting disease Gitelman syndrome4. As a key player in salt handling, the NCC regulates blood pressure and is the target of thiazide diuretics, which have been widely prescribed as first-line medications to treat hypertension for more than 60 years5-7. Here we determined the structures of human NCC alone and in complex with a commonly used thiazide diuretic using cryo-electron microscopy. These structures, together with functional studies, reveal major conformational states of the NCC and an intriguing regulatory mechanism. They also illuminate how thiazide diuretics specifically interact with the NCC and inhibit its transport function. Our results provide critical insights for understanding the Na-Cl cotransport mechanism of the NCC, and they establish a framework for future drug design and for interpreting disease-related mutations.

    View details for DOI 10.1038/s41586-023-05718-0

    View details for PubMedID 36792826

    View details for PubMedCentralID 46173

  • Bridge-Like Lipid Transfer Proteins (BLTPs) in C. elegans: From Genetics to Structures and Functions. Contact (Thousand Oaks (Ventura County, Calif.)) Pandey, T., Zhang, J., Wang, B., Ma, D. K. 2023; 6: 25152564231186489


    In eukaryotic cells, lipid transfer can occur at membrane contact sites (MCS) to facilitate the exchange of various lipids between two adjacent cellular organelle membranes. Lipid transfer proteins (LTPs), including shuttle LTP or bridge-like LTP (BLTP), transport lipids at MCS and are critical for diverse cellular processes, including lipid metabolism, membrane trafficking, and cell signaling. BLTPs (BLTP1-5, including the ATG2 and VPS13 family proteins) contain lipid-accommodating hydrophobic repeating beta-groove (RBG) domains that allow the bulk transfer of lipids through MCS. Compared with vesicular lipid transfer and shuttle LTP, BLTPs have been only recently identified. Their functions and regulatory mechanisms are currently being unraveled in various model organisms and by diverse approaches. In this review, we summarize the genetics, structural features, and biological functions of BLTP in the genetically tractable model organism C. elegans. We discuss our recent studies and findings on C. elegans LPD-3, a prototypical megaprotein ortholog of BLTP1, with identified lipid transfer functions that are evolutionarily conserved in multicellular organisms and in human cells. We also highlight areas for future research of BLTP using C. elegans and complementary model systems and approaches. Given the emerging links of BLTP to several human diseases, including Parkinson's disease and Alkuraya-Kucinskas syndrome, discovering evolutionarily conserved roles of BLTPs and their mechanisms of regulation and action should contribute to new advances in basic cell biology and potential therapeutic development for related human disorders.

    View details for DOI 10.1177/25152564231186489

    View details for PubMedID 37455813

  • A conserved megaprotein-based molecular bridge critical for lipid trafficking and cold resilience. Nature communications Wang, C., Wang, B., Pandey, T., Long, Y., Zhang, J., Oh, F., Sima, J., Guo, R., Liu, Y., Zhang, C., Mukherjee, S., Bassik, M., Lin, W., Deng, H., Vale, G., McDonald, J. G., Shen, K., Ma, D. K. 2022; 13 (1): 6805


    Cells adapt to cold by increasing levels of unsaturated phospholipids and membrane fluidity through conserved homeostatic mechanisms. Here we report an exceptionally large and evolutionarily conserved protein LPD-3 in C. elegans that mediates lipid trafficking to confer cold resilience. We identify lpd-3 mutants in a mutagenesis screen for genetic suppressors of the lipid desaturase FAT-7. LPD-3 bridges the endoplasmic reticulum (ER) and plasma membranes (PM), forming a structurally predicted hydrophobic tunnel for lipid trafficking. lpd-3 mutants exhibit abnormal phospholipid distribution, diminished FAT-7 abundance, organismic vulnerability to cold, and are rescued by Lecithin comprising unsaturated phospholipids. Deficient lpd-3 homologues in Zebrafish and mammalian cells cause defects similar to those observed in C. elegans. As mutations in BLTP1, the human orthologue of lpd-3, cause Alkuraya-Kucinskas syndrome, LPD-3 family proteins may serve as evolutionarily conserved highway bridges critical for ER-associated non-vesicular lipid trafficking and resilience to cold stress in eukaryotic cells.

    View details for DOI 10.1038/s41467-022-34450-y

    View details for PubMedID 36357390

  • Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1. Nature communications Zhang, J., Wang, Y. Y., Pan, Z. Q., Li, Y., Sui, J., Du, L. L., Ye, K. 2022; 13 (1): 3650


    Neighbor of BRCA1 (Nbr1) is a conserved autophagy receptor that provides cargo selectivity to autophagy. The four-tryptophan (FW) domain is a signature domain of Nbr1, but its exact function remains unclear. Here, we show that Nbr1 from the filamentous fungus Chaetomium thermophilum uses its FW domain to bind the α-mannosidase Ams1, a cargo of selective autophagy in both budding yeast and fission yeast, and delivers Ams1 to the vacuole by conventional autophagy in heterologous fission yeast. The structure of the Ams1-FW complex was determined at 2.2 Å resolution by cryo-electron microscopy. The FW domain adopts an immunoglobulin-like β-sandwich structure and recognizes the quaternary structure of the Ams1 tetramer. Notably, the N-terminal di-glycine of Ams1 is specifically recognized by a conserved pocket of the FW domain. The FW domain becomes degenerated in fission yeast Nbr1, which binds Ams1 with a ZZ domain instead. Our findings illustrate the protein binding mode of the FW domain and reveal the versatility of Nbr1-mediated cargo recognition.

    View details for DOI 10.1038/s41467-022-31439-5

    View details for PubMedID 35752625

  • Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1 EMBO JOURNAL Wang, Y., Zhang, J., Liu, X., Li, Y., Sui, J., Dong, M., Ye, K., Du, L. 2021; 40 (15): e107497


    In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.

    View details for DOI 10.15252/embj.2020107497

    View details for Web of Science ID 000665684600001

    View details for PubMedID 34169534

    View details for PubMedCentralID PMC8327946

  • Cryo-EM structure of fission yeast tetrameric alpha-mannosidase Ams1 FEBS OPEN BIO Zhang, J., Wang, Y., Du, L., Ye, K. 2020; 10 (11): 2437-2451


    Fungal α-mannosidase Ams1 and its mammalian homolog MAN2C1 hydrolyze terminal α-linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid-linked oligosaccharide donors. Ams1 is transported by selective autophagy into vacuoles. Here, we determine the tetrameric structure of Ams1 from the fission yeast Schizosaccharomyces pombe at 3.2 Å resolution by cryo-electron microscopy. Distinct from a low resolution structure of S. cerevisiae Ams1, S. pombe Ams1 has a prominent N-terminal tail that mediates tetramerization and an extra β-sheet domain. Ams1 shares a conserved active site with other enzymes in glycoside hydrolase family 38, to which Ams1 belongs, but contains extra N-terminal domains involved in tetramerization. The atomic structure of Ams1 reported here will aid understanding of its enzymatic activity and transport mechanism.

    View details for DOI 10.1002/2211-5463.12988

    View details for Web of Science ID 000579502400001

    View details for PubMedID 32981237

    View details for PubMedCentralID PMC7609781