Integrative solution structure of PTBP1-IRES complex reveals strong compaction and ordering with residual conformational flexibility

Georg Dorn, Christoph Gmeiner, Tebbe Vries, Emil Dedic, Mihajlo Novakovic, Fred F. Damberger, Christophe Maris, Esteban Finol, Chris P. Sarnowski, Joachim Kohlbrecher, Timothy J. Welsh, Sreenath Bolisetty, Raffaele Mezzenga, Ruedi Aebersold, Alexander Leitner, Maxim Yulikov (), Gunnar Jeschke () and Frédéric H.-T. Allain ()
Additional contact information
Georg Dorn: ETH Zürich
Christoph Gmeiner: ETH Zürich
Tebbe Vries: ETH Zürich
Emil Dedic: ETH Zürich
Mihajlo Novakovic: ETH Zürich
Fred F. Damberger: ETH Zürich
Christophe Maris: ETH Zürich
Esteban Finol: ETH Zürich
Chris P. Sarnowski: ETH Zürich
Joachim Kohlbrecher: Paul Scherrer Institut
Timothy J. Welsh: ETH Zürich
Sreenath Bolisetty: ETH Zürich
Raffaele Mezzenga: ETH Zürich
Ruedi Aebersold: ETH Zürich
Alexander Leitner: ETH Zürich
Maxim Yulikov: ETH Zürich
Gunnar Jeschke: ETH Zürich
Frédéric H.-T. Allain: ETH Zürich

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract RNA-binding proteins (RBPs) are crucial regulators of gene expression, often composed of defined domains interspersed with flexible, intrinsically disordered regions. Determining the structure of ribonucleoprotein (RNP) complexes involving such RBPs necessitates integrative structural modeling due to their lack of a single stable state. In this study, we integrate magnetic resonance, mass spectrometry, and small-angle scattering data to determine the solution structure of the polypyrimidine-tract binding protein 1 (PTBP1/hnRNP I) bound to an RNA fragment from the internal ribosome entry site (IRES) of the encephalomyocarditis virus (EMCV). This binding, essential for enhancing the translation of viral RNA, leads to a complex structure that demonstrates RNA and protein compaction, while maintaining pronounced conformational flexibility. Acting as an RNA chaperone, PTBP1 orchestrates the IRES RNA into a few distinct conformations, exposing the RNA stems outward. This conformational diversity is likely common among RNP structures and functionally important. Our approach enables atomic-level characterization of heterogeneous RNP structures.

Date: 2023
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DOI: 10.1038/s41467-023-42012-z

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