Extended Data Fig. 9: Extent of 40S head swivel on eIF3-bound 40S subunits is greater in ribosomes from infected cells (state 1; least rotated). | Nature Microbiology

Extended Data Fig. 9: Extent of 40S head swivel on eIF3-bound 40S subunits is greater in ribosomes from infected cells (state 1; least rotated).

From: Distinct non-canonical translation initiation modes arise for specific host and viral mRNAs during poxvirus-induced shutoff

Extended Data Fig. 9

a–c. 40S head swivel on eIF3-bound 40S particles from mock-infected cells. a. Fitting of the eIF3-bound 40S state (PDB 6ZVJ) into cryo-EM reconstruction of eIF3-bound 40S ribosomal subunit (state 1) isolated from mock-infected cells. Insets show focused views of good fits of the 40S body (RPS7, RPS13), but the model is slightly displaced in the 40S head (RPS25, RPS18, RPS5, RPS16). b. Focused views of RPS5 and RPS25 before (eIF3-bound 40S, PDB 6ZVJ) and after (best fit) separate rigid-body fitting of the 40S head into the cryo-EM density. Right, overlay of the before-and-after fitting reveals the trajectory of motion (tan, before; green, after). c. Separate rigid-body fitting of the 40S head into cryo-EM reconstruction of ribosomes from mock-infected cells reveals a 1.4° rotation of the head (green ribbon). Tan ribbon, standard fit from PDB 6ZVJ based on 40S body components. Rotation axis depicted as gray rod. d-f. 40S head swivel on eIF3-bound 40S particles from VacV-infected cells. d. Fitting of the eIF3-bound 40S state (PDB 6ZVJ) into cryo-EM reconstruction of eIF3-bound 40S ribosomal subunit (state 1) isolated from VacV-infected cells. Insets show focused views of good fits of the 40S body (RPS8), but the model is slightly displaced in the 40S head (RPS18, RPS12, RPS27a). e. Focused views of RPS18 before (eIF3-bound 40S, PDB 6ZVJ) and after (best fit) separate rigid-body fitting of the 40S head into the cryo-EM density. Right, overlay of the before-and-after fitting reveals the trajectory of motion (tan, before; green, after). f. Separate rigid-body fitting of the 40S head into cryo-EM reconstruction of virus-modified ribosomes reveals a 3.8° rotation of the head (green ribbon). Tan ribbon, standard fit from PDB 6ZVJ based on 40S body components. Rotation axis depicted as gray rod. g. Comparison of extent of 40S head swivel between mock-infected and VacV-infected cells. Structures of the 40S head in the least rotated state (state 1) after rigid body fitting (mock infected: teal, VacV infected: pink) overlayed against a previously published structure of eIF3-bound 40S particles (PDB 6ZVJ, tan), highlighting the increase in movement from VacV infected samples. Rotation axes of movement indicated by black rods.

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