scholarly journals Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Komal Soni ◽  
Georg Kempf ◽  
Karen Manalastas-Cantos ◽  
Astrid Hendricks ◽  
Dirk Flemming ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Binding Sites ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Closed Conformation ◽  
Open Conformation ◽  
Structural Database ◽  
Alu Rna ◽  
Species Specific ◽  
Protozoan Species

AbstractThe eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly ‘closed’ conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an ‘open’ Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.

scholarly journals Membrane binding of the bacterial signal recognition particle receptor involves two distinct binding sites

2006 ◽  
Vol 174 (5) ◽  
pp. 715-724 ◽  
Author(s):  
Sandra Angelini ◽  
Diana Boy ◽  
Emile Schiltz ◽  
Hans-Georg Koch
Keyword(s):  
Binding Sites ◽  
Protein Targeting ◽  
Cytoplasmic Membrane ◽  
Signal Recognition Particle ◽  
Membrane Association ◽  
Signal Recognition ◽  
Gtpase Activity ◽  
Signal Recognition Particle Receptor ◽  
Membrane Anchoring ◽  
Lipid Anchor

Cotranslational protein targeting in bacteria is mediated by the signal recognition particle (SRP) and FtsY, the bacterial SRP receptor (SR). FtsY is homologous to the SRα subunit of eukaryotes, which is tethered to the membrane via its interaction with the membrane-integral SRβ subunit. Despite the lack of a membrane-anchoring subunit, 30% of FtsY in Escherichia coli are found stably associated with the cytoplasmic membrane. However, the mechanisms that are involved in this membrane association are only poorly understood. Our data indicate that membrane association of FtsY involves two distinct binding sites and that binding to both sites is stabilized by blocking its GTPase activity. Binding to the first site requires only the NG-domain of FtsY and confers protease protection to FtsY. Importantly, the SecY translocon provides the second binding site, to which FtsY binds to form a carbonate-resistant 400-kD FtsY–SecY translocon complex. This interaction is stabilized by the N-terminal A-domain of FtsY, which probably serves as a transient lipid anchor.

scholarly journals Ribosome Binding to and Dissociation from Translocation Sites of the Endoplasmic Reticulum Membrane

2006 ◽  
Vol 17 (9) ◽  
pp. 3860-3869 ◽  
Author(s):  
Julia Schaletzky ◽  
Tom A. Rapoport
Keyword(s):  
Endoplasmic Reticulum ◽  
Binding Sites ◽  
Signal Recognition Particle ◽  
Structural Data ◽  
Endoplasmic Reticulum Membrane ◽  
Signal Recognition ◽  
Ribosome Binding ◽  
High Affinity ◽  
Chain Complexes ◽  
Nascent Chain

We have addressed how ribosome-nascent chain complexes (RNCs), associated with the signal recognition particle (SRP), can be targeted to Sec61 translocation channels of the endoplasmic reticulum (ER) membrane when all binding sites are occupied by nontranslating ribosomes. These competing ribosomes are known to be bound with high affinity to tetramers of the Sec61 complex. We found that the membrane binding of RNC–SRP complexes does not require or cause the dissociation of prebound nontranslating ribosomes, a process that is extremely slow. SRP and its receptor target RNCs to a free population of Sec61 complex, which associates with nontranslating ribosomes only weakly and is conformationally different from the population of ribosome-bound Sec61 complex. Taking into account recent structural data, we propose a model in which SRP and its receptor target RNCs to a Sec61 subpopulation of monomeric or dimeric state. This could explain how RNC–SRP complexes can overcome the competition by nontranslating ribosomes.

scholarly journals The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14

1997 ◽  
Vol 16 (13) ◽  
pp. 3757-3766 ◽  
Author(s):  
Darcy E.A. Birse ◽  
Ulrike Kapp ◽  
Katharina Strub ◽  
Stephen Cusack ◽  
Anders Åberg
Keyword(s):  
Crystal Structure ◽  
Rna Binding ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Alu Rna

scholarly journals Closed headpiece of integrin αIIbβ3 and its complex with an αIIbβ3-specific antagonist that does not induce opening

Blood ◽  
2010 ◽  
Vol 116 (23) ◽  
pp. 5050-5059 ◽  
Author(s):  
Jieqing Zhu ◽  
Jianghai Zhu ◽  
Ana Negri ◽  
Davide Provasi ◽  
Marta Filizola ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Basis ◽  
Plasma Proteins ◽  
Gel Filtration ◽  
Integrin Αiibβ3 ◽  
Closed Conformation ◽  
Small Molecule Antagonist ◽  
Open Conformation ◽  
Specific Antagonist ◽  
Species Specific

Abstract The platelet integrin αIIbβ3 is essential for hemostasis and thrombosis through its binding of adhesive plasma proteins. We have determined crystal structures of the αIIbβ3 headpiece in the absence of ligand and after soaking in RUC-1, a novel small molecule antagonist. In the absence of ligand, the αIIbβ3 headpiece is in a closed conformation, distinct from the open conformation visualized in presence of Arg-Gly-Asp (RGD) antagonists. In contrast to RGD antagonists, RUC-1 binds only to the αIIb subunit. Molecular dynamics revealed nearly identical binding. Two species-specific residues, αIIb Y190 and αIIb D232, in the RUC-1 binding site were confirmed as important by mutagenesis. In sharp contrast to RGD-based antagonists, RUC-1 did not induce αIIbβ3 to adopt an open conformation, as determined by gel filtration and dynamic light scattering. These studies provide insights into the factors that regulate integrin headpiece opening, and demonstrate the molecular basis for a novel mechanism of integrin antagonism.

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