2025-01-29 REL PDBe PDBe PDBe 2024-04-10 2025-01-29 2025-01-29 2025-01-29 Bill & Melinda Gates Foundation RG.IMCB.I8-TSA-083 United States Poliovirus type 1 (strain Mahoney) expanded conformation stabilised virus-like particle (PV1 SC6b) from a yeast expression system. Bahar MW Sherry L Stonehouse NJ Rowlands DJ Fry EE Stuart DI Capsid protein, virus-like particle, vaccine, VIRUS LIKE PARTICLE Sherry L Bahar MW Porta C Fox H Grehan K Nasta V Duyvesteyn HME De Colibus L Marsian J Murdoch I Ponndorf D Kim SR Shah S Carlyle S Swanson JJ Matthews S Nicol C Lomonossoff GP Macadam AJ Fry EE Stuart DI Stonehouse NJ Rowlands DJ Recombinant expression systems for production of stabilised virus-like particles as next-generation polio vaccines. Nat Commun UK 16 831 831 2025 39827284 doi:10.1038/s41467-025-56118-z 2041-1723 9ez0 FULLOVERLAP Human poliovirus 1 Mahoney Human poliovirus 1 Mahoney 0 1 2 3
Recombinantly expressed virus-like particle of poliovirus type 1 (Mahoney strain).
Human poliovirus 1 Mahoney Mahoney Homo sapiens 5.84 Virus shell 1 310.0 1 VIRUS-LIKE PARTICLE SEROTYPE false true Capsid protein VP1 Human poliovirus 1 Mahoney 0.033447586 1 Komagataella pastoris LEVO GLGQMLESMIDNTVRETVGAATSRDALPNTEASGPTHSKEIPALTAVETGATNPLVPSDTVQTRHVVQHRSRSESSIESF FARGACVTIMTVDNPASTTNKDKLFAVWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTETNNGHALNQVYQIMYV PPGAPVPEKWDDYTWQTSSNPSIFYTYGTAPARISVPYVGISNAYSHFYDGFSKVPLKDQSAALGDSLYGAASLNDFGIL AVRVVNDPNPTKVTSKIRVYLKPKHIRVWCPRPPRAVAYYGPGVDYKDGTLTPLSTKDLTTY P03300 Capsid protein VP0 Human poliovirus 1 Mahoney 0.037465811999999994 1 Komagataella pastoris LEVO MGAQVSSQKVGAHENSNGAYGGSTINYTTINYYRDSASNAASKQDFSQDPSKFTEPIKDVLIKTAPMLNSPNIEACGYSD RVLQLTLGNSTITAQEAANSVVAYGRWPEYLRDSEANPVDQPTEPEVAACRFYTLDTVSWTKESRGWWWKLPDALRDMGL FGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSNTTTMHTSYQNANPGEKGGTFTGTFTPDNNQTSPA RRFCPVDYLLGNGTLLGNAFVFPHQIINLRTNNCATLVLPYVNSLSIDSMVKHNNWGIAILPLAPLNFASESSPEIPITL TIAPMCCEFNGLRNITLPRLQ P03300 Capsid protein VP3 Human poliovirus 1 Mahoney 0.026550548999999996 1 Komagataella pastoris LEVO GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEIDTMIPFDLSATKKNTMEMYRVRLSDKPHTDD PILCLSLSPASDPRLSHTMLGEILNYYTHWAGSLKFTFMFCGSMMATGKLLVSYAPPGADPPKKRKEAMLGTHVIWDIGL QSSCTMVVPWISNTTYRLTIDDSFTEGGYISVFYQTRIVVPLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKALAQ P03300 singleParticle particle 1.1 7.0 1.0 DPBS 20.0 EDTA
1 x DPBS, 20 mM EDTA, pH 7.0
 C-flat-2/1 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE-PROPANE 100 277.15 FEI VITROBOT MARK IV
3-4 ul of sample double blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV..
Sample purified by sucrose density gradient ultracentrifugation.
 FEI TITAN KRIOS FLOOD BEAM DARK FIELD FIELD EMISSION GUN 300 100.0 2.7 0.8 2.9 130000.0 47619.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-30 1 4282 6.0 41.14
Pixel sampling was 1.05 A/pixel. Energy filter was Gatan GIF Quantum.
 1 4578
Particle picking was performed using Xmipp as part of the Scipion software framework.
 EMD-3747
Startup model was low pass filtered to 60 Angstroms.
 1 I BACK PROJECTION 3.3 FSC 0.143 CUT-OFF
Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -76.9 Angstroms.
2428 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 4 937.0
3748 particles used for 3D classification.
 emd_50066.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.99997 419.99997 419.99997 90.0 90.0 90.0 X Y Z -0.07139318 0.1464879 0.0012919956 0.008883472 1.05 1.05 1.05 0.037 AUTHOR 1HXS PDB experimental model RIGID BODY FIT
Initial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine. Model fit was optimised using molecular dynamics flexible fitting using Namdinator software.
Cross-correlation coefficient REAL emd_50066_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.99997 419.99997 419.99997 90.0 90.0 90.0 X Y Z -0.026197208 0.043950833 0.0003099096 0.004291449 1.05 1.05 1.05 AUTHOR emd_50066_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 419.99997 419.99997 419.99997 90.0 90.0 90.0 X Y Z -0.037286833 0.07575296 0.00029990057 0.0043202927 1.05 1.05 1.05 AUTHOR