Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.
Journal, issue, pages	Commun Chem, Vol. 7, Issue 1, Page 14, Year 2024
Publish date	Jan 17, 2024
Authors	Luka Kavčič / Andreja Kežar / Neža Koritnik / Magda Tušek Žnidarič / Tajda Klobučar / Žiga Vičič / Franci Merzel / Ellie Holden / Justin L P Benesch / Marjetka Podobnik /
PubMed Abstract	The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid ...The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
External links	Commun Chem / PubMed:38233506 / PubMed Central
Methods	EM (helical sym.) / EM (single particle)
Resolution	2.41 - 12.75 Å
Structure data	17046 8opa EMDB-17046, PDB-8opa: Virus-like Particle based on PVY coat protein with stacked-ring architecture Method: EM (helical sym.) / Resolution: 3.34 Å 17047 8opb EMDB-17047, PDB-8opb: Virus-like Particle based on PVY coat protein with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 3.58 Å 17048 8opc EMDB-17048, PDB-8opc: Virus-like Particle based on PVY coat protein with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 2.99 Å 17049 8opd EMDB-17049, PDB-8opd: Virus-like Particle based on PVY coat protein with dC40 deletion with stacked-ring architecture Method: EM (helical sym.) / Resolution: 3.5 Å 17050 8ope EMDB-17050, PDB-8ope: Virus-like Particle based on PVY coat protein with dC40 deletion with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 3.09 Å 17051 8opf EMDB-17051, PDB-8opf: Virus-like Particle based on PVY coat protein with dC60 deletion with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 2.83 Å 17052 8opg EMDB-17052, PDB-8opg: Virus-like Particle based on PVY coat protein with dC79 deletion with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 3.2 Å 17053 8oph EMDB-17053, PDB-8oph: Head-to-tail double ring assembly from truncated PVY coat protein Method: EM (single particle) / Resolution: 2.93 Å EMDB-17054: RNA-free helical assembly from truncated PVY coat protein Method: EM (helical sym.) / Resolution: 3.59 Å EMDB-17055: Stacked-ring assembly from truncated PVY coat protein Method: EM (single particle) / Resolution: 3.62 Å EMDB-17056: Stacked-ring assembly from truncated PVY coat protein with L99C mutation Method: EM (helical sym.) / Resolution: 3.45 Å EMDB-17057: Helical assembly from truncated PVY coat protein with L99C mutation Method: EM (helical sym.) / Resolution: 3.06 Å EMDB-17058: Helical assembly from truncated PVY coat protein with K153E mutation Method: EM (helical sym.) / Resolution: 3.41 Å EMDB-17059: Cross-shaped junction assembly from truncated PVY coat protein with E150C mutation Method: EM (single particle) / Resolution: 3.6 Å EMDB-17060: Global refinement map of head-to-head double ring assembly from truncated PVY coat protein with K176E mutation Method: EM (single particle) / Resolution: 4.56 Å EMDB-17061: Local refinement map of head-to-head double ring assembly from truncated PVY coat protein with K176E mutation Method: EM (single particle) / Resolution: 3.82 Å 17062 8opj EMDB-17062, PDB-8opj: Global refinement of cubic assembly from truncated PVY coat protein with K176C mutation Method: EM (single particle) / Resolution: 2.99 Å 17063 8opk EMDB-17063, PDB-8opk: Local refinement of cubic assembly from truncated PVY coat protein with K176C mutation Method: EM (single particle) / Resolution: 3.16 Å EMDB-17064: Spherical assembly from truncated PVY coat protein with K177E mutation Method: EM (single particle) / Resolution: 12.75 Å EMDB-17065: Cubic assembly from truncated PVY coat protein with K176C mutation and removed His tag Method: EM (single particle) / Resolution: 4.16 Å EMDB-17066: Virus-like Particle based on PVY coat protein with L99C and K176C mutation with stacked-ring architecture Method: EM (helical sym.) / Resolution: 3.18 Å EMDB-17067: Virus-like Particle based on PVY coat protein with L99C and K176C mutation with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 3.2 Å EMDB-17068: Virus-like Particle based on PVY coat protein with E150C and G193C mutation with stacked-ring architecture Method: EM (helical sym.) / Resolution: 3.75 Å EMDB-17069: Virus-like Particle based on PVY coat protein with E150C and G193C mutation with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 3.15 Å EMDB-17070: Virus-like Particle based on PVY coat protein with S39C and E72C mutation with stacked-ring architecture Method: EM (helical sym.) / Resolution: 3.83 Å EMDB-17071: Virus-like Particle based on PVY coat protein with S39C and E72C mutation with RNA-free helical architecture Method: EM (helical sym.) / Resolution: 3.69 Å 17072 8opl EMDB-17072, PDB-8opl: Virus-like Particle based on PVY coat protein with T43C and D136C mutation with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 2.41 Å EMDB-17073: Virus-like Particle based on PVY coat protein with D136C mutation with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 3.46 Å EMDB-17074: Virus-like Particle based on PVY coat protein with R46A mutation with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 2.62 Å EMDB-17075: Virus-like Particle based on PVY coat protein with E139A mutation with helical architecture encapsidating ssRNA Method: EM (helical sym.) / Resolution: 3.17 Å
Source	potato virus y strain ntn
Keywords	VIRUS LIKE PARTICLE / stacked-ring / VLP / Potyvirus / PVY / helical / RNA-free / ssRNA / dC40 / dC60 / dC79 / H2T double ring / trCP / cubes / K176C