6CKU

Solution structure of the zebrafish granulin AaE

Summary for 6CKU

• Entry DOI: 10.2210/pdb6cku/pdb
• NMR Information: BMRB: 30422
• Descriptor: Granulin-AaE (1 entity in total)
• Functional Keywords: granulin/epithelin module, beta-hairpin stack, progranulins, signaling protein
• Biological source: Danio rerio (Zebrafish)
• Total number of polymer chains: 1
• Total formula weight: 5698.43

Authors

Wang, P.,Ni, F. (deposition date: 2018-02-28, release date: 2018-06-13, Last modification date: 2024-11-13)

Primary citation

Wang, P.,Chitramuthu, B.,Bateman, A.,Bennett, H.P.J.,Xu, P.,Ni, F.
Structure dissection of zebrafish progranulins identifies a well-folded granulin/epithelin module protein with pro-cell survival activities.
Protein Sci., 27:1476-1490, 2018

PubMed Abstract: The ancient and pluripotent progranulins contain multiple repeats of a cysteine-rich sequence motif of ∼60 amino acids, called the granulin/epithelin module (GEM) with a prototypic structure of four β-hairpins zipped together by six inter-hairpin disulfide bonds. Prevalence of this disulfide-enforced structure is assessed here by an expression screening of 19 unique GEM sequences of the four progranulins in the zebrafish genome, progranulins 1, 2, A and B. While a majority of the expressed GEM peptides did not exhibit uniquely folded conformations, module AaE from progranulin A and AbB from progranulin B were found to fold into the protopypic 4-hairpin structure along with disulfide formation. Module AaE has the most-rigid three-dimensional structure with all four β-hairpins defined using high-resolution (H- N) NMR spectroscopy, including 492 inter-proton nuclear Overhauser effects, 23 J(HN,H ) coupling constants, 22 hydrogen bonds as well as 45 residual dipolar coupling constants. Three-dimensional structure of AaE and the partially folded AbB re-iterate the conformational stability of the N-terminal stack of two beta-hairpins and varying degrees of structural flexibility for the C-terminal half of the 4-hairpin global fold of the GEM repeat. A cell-based assay demonstrated a functional activity for the zebrafish granulin AaE in promoting the survival of neuronal cells, similarly to what has been found for the corresponding granulin E module in human progranulin. Finally, this work highlights the remaining challenges in structure-activity studies of proteins containing the GEM repeats, due to the apparent prevalence of structural disorder in GEM motifs despite potentially a high density of intramolecular disulfide bonds.

PubMed: 29732682
DOI: 10.1002/pro.3441

Experimental method

SOLUTION NMR