Molecular architecture of the yeast Elongator complex reveals an unexpected asymmetric subunit arrangement

• Published in: EMBO reports 2017-02, Vol.18 (2), p.280-291
• Main Authors: Setiaputra, Dheva T, Cheng, Derrick TH, Lu, Shan, Hansen, Jesse M, Dalwadi, Udit, Lam, Cindy HY, To, Jeffrey L, Dong, Meng‐Qiu, Yip, Calvin K
• Format: Article
• Language: English
• Subjects: Conserved Sequence; Electron microscopy; Elongator; EMBO36; EMBO40; Evolution, Molecular; Fungal Proteins - chemistry; Fungal Proteins - genetics; Fungal Proteins - metabolism; Histone Acetyltransferases - chemistry; Histone Acetyltransferases - genetics; Histone Acetyltransferases - metabolism; Mass Spectrometry; Microscopy; Models, Molecular; Multiprotein Complexes - chemistry; Multiprotein Complexes - metabolism; Multiprotein Complexes - ultrastructure; Protein Binding; Protein Conformation; Protein Multimerization; Protein Subunits - chemistry; Protein Subunits - genetics; Protein Subunits - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Scientific imaging; Sequence Deletion; structure; Structure-Activity Relationship; tRNA modification; Yeast; Yeasts
• ISSN: 1469-221X; 1469-3178
• DOI: 10.15252/embr.201642548

Elongator is a ~850 kDa protein complex involved in multiple processes from transcription to tRNA modification. Conserved from yeast to humans, Elongator is assembled from two copies of six unique subunits (Elp1 to Elp6). Despite the wealth of structural data on the individual subunits, the overall architecture and subunit organization of the full Elongator and the molecular mechanisms of how it exerts its multiple activities remain unclear. Using single‐particle electron microscopy (EM), we revealed that yeast Elongator adopts a bilobal architecture and an unexpected asymmetric subunit arrangement resulting from the hexameric Elp456 subassembly anchored to one of the two Elp123 lobes that form the structural scaffold. By integrating the EM data with available subunit crystal structures and restraints generated from cross‐linking coupled to mass spectrometry, we constructed a multiscale molecular model that showed the two Elp3, the main catalytic subunit, are located in two distinct environments. This work provides the first structural insights into Elongator and a framework to understand the molecular basis of its multifunctionality. Synopsis The conserved Elongator complex specifically modifies tRNAs. Here, the molecular architecture and subunit organization of yeast holo‐Elongator are reported based on single‐particle EM and cross‐linking mass spectrometry. Negative stain electron microscopy analysis revealed that yeast holo‐Elongator adopts an asymmetric, bilobal architecture with the heterohexameric Elp456 subcomplex binding to only one of two Elp123 wing‐shaped lobes. Cross‐linking coupled to mass spectrometry analysis identified the network of interactions among Elongator subunits and showed that Elp1, Elp3, and Elp4 form the structural core. Elongator is capable of incorporating a second copy of Elp456, and its stoichiometry might be controlled by the available pool of Elp456 in the cytoplasm. Graphical Abstract The conserved Elongator complex specifically modifies tRNAs. Here, the molecular architecture and subunit organization of yeast holo‐Elongator are reported based on single‐particle EM and cross‐linking mass spectrometry.