2024-03-06 REL RCSB RCSB RCSB 2020-01-05 2020-01-29 2020-08-12 2024-03-06 Bill & Melinda Gates Foundation OPP1115782 United States De novo designed icosahedral nanoparticle I53_dn5 Antanasijevic A Ward AB De novo, Nanoparticle, DE NOVO PROTEIN Ueda G Antanasijevic A Fallas JA Sheffler W Copps J Ellis D Hutchinson GB Moyer A Yasmeen A Tsybovsky Y Park YJ Bick MJ Sankaran B Gillespie RA Brouwer PJ Zwart PH Veesler D Kanekiyo M Graham BS Sanders RW Moore JP Klasse PJ Ward AB King NP Baker D Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens. Elife US 9 2020 32748788 doi:10.7554/eLife.57659 2050-084X 6vfj FULLOVERLAP De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP De novo designed nanoparticle of icosahedral symmetry I53_dn5_NP 0 1 2
Self-assembling nanoparticle of icosahedral symmetry
synthetic construct 1.96 I53_dn5B synthetic construct 0.015356008999999999 1 Escherichia coli BL21(DE3) LEVO MEEAELAYLLGELAYKLGEYRIAIRAYRIALKRDPNNAEAWYNLGNAYYKQGRYREAIEYYQKALELDPNNAEAWYNLGN AYYERGEYEEAIEYYRKALRLDPNNADAMQNLLNAKMREELEHHHHHH I53_dn5A synthetic construct 0.017215148 1 Escherichia coli BL21(DE3) LEVO MGKYDGSKLRIGILHARWNAEIILALVLGALKRLQEFGVKRENIIIETVPGSFELPYGSKLFVEKQKRLGKPLDAIIPIG VLIKGSTMHFEYICDSTTHQLMKLNFELGIPVIFGVLTCLTDEQAEARAGLIEGKMHNHGEDWGAAAVEMATKFN singleParticle particle 1.9 7.4 25.0 Tris-HCl 150.0 NaCl Sodium Chloride
Fresh TBS buffer, 0.2um filtered, 0.06mM DDM detergent added immediately before freezing
 CARBON HOLEY 11.0
unspecified
 ETHANE 100 283 FEI VITROBOT MARK IV
0.06mM DDM detergent (from an 8X stock) added immediately before freezing.
Nanoparticle was generated by co-expression of two components (A and B) in E coli. Assembled particles purified using a combination of Ni-affinity chromatography and gel filtration chromatography.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 1.5 29000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 70.0 90.0 GATAN K2 SUMMIT (4k x 4k) COUNTING 1 1548 50.4 1 207651
Ab Initio generated model from cryoSPARC
 1 I BACK PROJECTION 5.35 FSC 0.143 CUT-OFF RELION 3.0 31353 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 10 RELION 3.0 emd_21174.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 412.0 412.0 412.0 90.0 90.0 90.0 X Y Z -0.014618222 0.04184899 0.00016296933 0.0028055245 1.03 1.03 1.03 0.015 AUTHOR I53_dn5 Nanoparticle Map OTHER
Icosahedral nanoparticle I53_dn5 model was docked into a reconstructed map using UCSF Chimera and Rosetta relaxed refinement was applied to relax the model into the map.
REAL emd_21174_msk_1.map emd_21174_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 412.0 412.0 412.0 90.0 90.0 90.0 X Y Z -0.008216668 0.020141914 0.00020194055 0.002139751 1.03 1.03 1.03 AUTHOR I53_dn5 Nanoparticle Half-Map 1 emd_21174_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 412.0 412.0 412.0 90.0 90.0 90.0 X Y Z -0.0076485877 0.019397436 0.0001239981 0.0021397094 1.03 1.03 1.03 AUTHOR I53_dn5 Nanoparticle Half-Map 2