3JCI

2.9 Angstrom Resolution Cryo-EM 3-D Reconstruction of Close-packed PCV2 Virus-like Particles

Summary for 3JCI

• Entry DOI: 10.2210/pdb3jci/pdb
• EMDB information: 6555
• Descriptor: Capsid protein (1 entity in total)
• Functional Keywords: de novo initial model, consensus criterion, gold-standard fsc, true fsc, cross-validation, virus like particle
• Biological source: Porcine circovirus-2 (PCV2)
• Total number of polymer chains: 1
• Total formula weight: 21999.76

Authors

Liu, Z.,Guo, F.,Wang, F.,Li, T.C.,Jiang, W. (deposition date: 2015-12-13, release date: 2016-02-03, Last modification date: 2024-02-21)

Primary citation

Liu, Z.,Guo, F.,Wang, F.,Li, T.C.,Jiang, W.
2.9 angstrom Resolution Cryo-EM 3D Reconstruction of Close-Packed Virus Particles.
Structure, 24:319-328, 2016

PubMed Abstract: Single-particle cryoelectron microscopy typically discards close-packed particle images as unusable data. Here, we report an image processing strategy and case study of obtaining near-atomic resolution 3D reconstructions from close-packed particles. Multiple independent de novo initial models were constructed to determine and cross-validate the particle parameters. The particles with consistent views were further refined including not only Euler angles and center positions but also defocus, astigmatism, beam tilt, and overall and anisotropic magnification. We demonstrated this strategy with a 2.9 Å resolution reconstruction of a 1.67 MDa virus-like particle of a circovirus, PCV2, recorded on 86 photographic films. The map resolution was further validated with a phase-randomization test and local resolution assessment, and the atomic model was validated with MolProbity and EMRinger. Close-packed virus particles were thus shown not only to be useful for high-resolution 3D reconstructions but also to allow data collection at significantly improved throughput for near-atomic resolution reconstructions.

PubMed: 26777413
DOI: 10.1016/j.str.2015.12.006

Experimental method

ELECTRON MICROSCOPY (2.9 Å)