8EM2

Cryo-EM structure of the human GDH/6PGL endoplasmic bifunctional protein

Summary for 8EM2

• Entry DOI: 10.2210/pdb8em2/pdb
• EMDB information: 23429 28232
• Descriptor: GDH/6PGL endoplasmic bifunctional protein, 2-acetamido-2-deoxy-beta-D-glucopyranose (2 entities in total)
• Functional Keywords: h6pd, oxidoreductase, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 178445.57

Authors

Su, C.C. (deposition date: 2022-09-26, release date: 2023-05-03, Last modification date: 2023-11-15)

Primary citation

Su, C.C.,Lyu, M.,Zhang, Z.,Miyagi, M.,Huang, W.,Taylor, D.J.,Yu, E.W.
High-resolution structural-omics of human liver enzymes.
Cell Rep, 42:112609-112609, 2023

PubMed Abstract: We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.

PubMed: 37289586
DOI: 10.1016/j.celrep.2023.112609

Experimental method

ELECTRON MICROSCOPY (3.02 Å)