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TitleStructural basis of signal peptide recognition by the signal peptidase complex.
Journal, issue, pagesNat Commun, Year 2026
Publish dateMay 22, 2026
AuthorsA Manuel Liaci / Dimitrios Vismpas / Lisbeth R Kjølbye / Ioannis Skalidis / Gilberto P Pereira / Adrian Fujiet Koh / Mariska Gröllers-Mulderij / Abhay Kotecha / Paulo C T Souza / Friedrich Förster /
PubMed AbstractThe signal peptidase complex (SPC) is responsible for cleaving signal peptides (SPs) from approximately 10% of the human proteome. SPs are characterized by a tripartite structure, consisting of an N- ...The signal peptidase complex (SPC) is responsible for cleaving signal peptides (SPs) from approximately 10% of the human proteome. SPs are characterized by a tripartite structure, consisting of an N-terminal n-region, a central helical h-region and a C-terminal c-region, each defined by rather general chemical properties rather than strict sequence conservation. Despite their sequence diversity, SPC recognizes and processes SPs with exquisite specificity. Here, we present a 2.6 Å cryo-EM map of the human SPC-A, one of two SPC paralogs, bound to a model SP. The c-region binds to a hydrophobic binding groove near the active site, a narrow gate marks the transition from c- to h-region, and the h-region localizes in a transmembrane (TM) window. Substrate engagement stabilizes N- and C-terminal helices of Sec11A, which frame the SP and are unresolved in the apo structure. Molecular dynamics (MD) simulations confirm a stable hydrogen-bonding network at the c-region and indicate dynamic interactions within a thinned lipid environment at the TM window. AlphaFold modeling supports this binding mode across physiological SPs. Collectively, our structural and computational analyses explain how the SPC achieves its specificity by combining the selectivity of the luminal binding groove and of the transmembrane window.
External linksNat Commun / PubMed:42173868
MethodsEM (single particle)
Resolution2.6 - 4.2 Å
Structure data

54010

9rjb

EMDB-54010, PDB-9rjb:
Human Signal Peptidase in complex with artificial Signal Peptide L11
Method: EM (single particle) / Resolution: 2.6 Å

54011

9rjc

EMDB-54011, PDB-9rjc:
Apo Structure of the Human Signal Peptidase
Method: EM (single particle) / Resolution: 4.2 Å

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / Signal Peptidase Complex / Signal Peptide / protein biogenesis / secretory pathway / membrane thinning

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