9GDX

SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses

Summary for 9GDX

• Entry DOI: 10.2210/pdb9gdx/pdb
• EMDB information: 51279
• Descriptor: Spike glycoprotein,Fibritin (1 entity in total)
• Functional Keywords: sars-cov-2, spike protein, temperature dependence, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2; More
• Total number of polymer chains: 3
• Total formula weight: 408428.11

Authors

Herreros, D.,Mata, C.P.,Noddings, C.,Irene, D.,Agard, D.A.,Tsai, M.-D.,Sorzano, C.O.S.,Carazo, J.M. (deposition date: 2024-08-06, release date: 2024-10-30, Last modification date: 2025-05-07)

Primary citation

Herreros, D.,Mata, C.P.,Noddings, C.,Irene, D.,Krieger, J.,Agard, D.A.,Tsai, M.D.,Sorzano, C.O.S.,Carazo, J.M.
Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Nat Commun, 16:3751-3751, 2025

PubMed Abstract: Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformations of macromolecules. Traditional methods assume discrete conformations, while newer algorithms estimate conformational landscapes representing the different structural states a biomolecule explores. This work presents HetSIREN, a deep learning-based method that can fully reconstruct or refine a CryoEM volume in real space based on the structural information summarized in a conformational latent space. HetSIREN is defined as an accurate space-based method that allows spatially focused analysis and the introduction of sinusoidal hypernetworks with proven high analytics capacities. Continuing with innovations, HetSIREN can also refine the images' pose while conditioning the network with additional constraints to yield cleaner high-quality volumes, as well as addressing one of the most confusing issues in heterogeneity analysis, as it is the fact that structural heterogeneity estimations are entangled with pose estimation (and to a lesser extent with CTF estimation) thanks to its decoupling architecture.

PubMed: 40263313
DOI: 10.1038/s41467-025-59135-0

Experimental method

ELECTRON MICROSCOPY (2.8 Å)