2025-01-29 REL PDBe PDBe PDBe 2024-04-28 2025-01-29 2025-01-29 2025-01-29 Bill & Melinda Gates Foundation RG.IMCB.I8-TSA-083 United States Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a mammalian expression system. Bahar MW Porta C Fry EE Stuart DI Capsid protein, 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 9f59 FULLOVERLAP Poliovirus 2 Poliovirus 2 0 1 2 3
Recombinantly expressed virus-like particle of poliovirus type 2 (MEF-1 strain).
Poliovirus 2 MEF-1 Homo sapiens 5.81 Virus shell 1 310.0 1 VIRUS-LIKE PARTICLE SEROTYPE false true Capsid protein VP1 Poliovirus 2 MEF-1 0.033105246 1 Mesocricetus auratus LEVO GLGDLIEGVVEGVTRNALTPLTPANNLPDTQSSGPAHSKETPALTAVETGATNPLVPSDTVQTRHVIQKRTRSESTVESF FARGACVAIIEVDNDAPTKRASKLFSIWKITYKDTVQLRRKLEFFTYSRFDMELTFVVTSNYTDANNGHALNQVYQIMYI PPGAPIPGKWNDYTWQTSSNPSLFYTYGAPPARISVPYVGIANAYSHFYDGFAKVPLAGQASTEGDSLYGAASLNDFGSL AVRVVNDHNPTKLTSKIRVYMKPKHVRVWCPRPPRAVPYYGPGVDYKDGLAPLPEKGLTTY P06210 Capsid protein VP0 Poliovirus 2 MEF-1 0.037398815999999994 1 Mesocricetus auratus LEVO MGAQVSSQKVGAHENSNRAYGGSTINYTTINYYRDSASNAASKQDFAQDPSKFTEPVKDVLIKTAPTLNSPNIEACGYSD RVMQLTLGNSTITTQEAANSVVAYGRWPEYIKDSEANPVDQPTEPAVAACRFYTLDTVTWRKESRGWWWKLPDALKDMGL FGQNMFYHYLGRAGYTVHVQCNASKFHQGALGVFAVPEMCLAGDSTTHMFTKYENANPGEKGGEFKGSFTLDTNATNPAR NFCPVDYLFGSGVLAGNAFVYPHQIINLRTNNCATLVLPYVNSLSIDSMTKHNNWGIAILPLAPLDFATESSTEIPITLT IAPMCCEFNGLRNITVPRTQ P06210 Capsid protein VP3 Poliovirus 2 MEF-1 0.026457322 1 Mesocricetus auratus LEVO GLPVLNTPGSNQYLTADNYQSPCAIPEFDVTPPIDIPGEVRNMMELAEIDTMIPLNLTNQRKNTMDMYRVELNDAAHSDT PILCLSLSPASDPRLAHTMLGEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGAEAPKSRKEAMLGTHVIWDIGL QSSCTMVVPWISNTTYRLTINDSFTEGGYISMFYQTRVVVPLSTPRKMDILGFVSACNDFSVRLLRDTTHISQEAMPQ P06210 SPHINGOSINE 0.000299492 1 SPH water 1.8015e-05 123 HOH singleParticle particle 0.62 7.0 1.0 DPBS 20.0 EDTA
1 x DPBS, 20 mM EDTA, pH 7.0
 EMS Lacey Carbon COPPER 400 CARBON LACEY 3.0 GLOW DISCHARGE AIR
The exact grid type was the Ultra-thin carbon support film, 3nm - on lacey carbon. Product code AGS187-4 from Agar Scientific.
 ETHANE-PROPANE 100 277.15 FEI VITROBOT MARK IV
4 ul of sample 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 47393.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 10
Gatan GIF Quantum energy filter.
Preliminary grid screening was performed on a Glacios 200 kV microscope.
GATAN K2 SUMMIT (4k x 4k) COUNTING 1-40 1 1331 10.0 39.08
Pixel sampling was 1.055 A/pixel.
 1
EER files were fractionated by 40 fractions.
18864
Particle picking was performed using the template picker in CryoSPARC.
 Five independent 3D models generated in cryoSPARC using ab-initio reconstruction and applying icosahedral symmetry. 1 I BACK PROJECTION 2.3 FSC 0.143 CUT-OFF cryoSPARC 4.2.1 Homogeneous reconstruction
Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -67.7 Angstrom squared.
18378 RANDOM ASSIGNMENT cryoSPARC 4.2.1 ab initio reconstruction
cryoSPARC ab-initio reconstruction uses stochastic gradient descent.
 MAXIMUM LIKELIHOOD cryoSPARC 4.2.1 Homogeneous reconstruction
Final angle assignment was achieved by homogeneous refinement procedures in cryoSPARC, which uses branch-and-bound maximum likelihood.
 3 6144.0 cryoSPARC 4.2.1 Heterogeneous reconstruction
Final classification was performed using the heterogeneous reconstruction job in cryoSPARC. 18433 particles used for heterogeneous reconstruction.
 emd_50189.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 506.39996 506.39996 506.39996 90.0 90.0 90.0 X Y Z -1.308588 2.5221105 0.010620236 0.14901097 1.055 1.055 1.055 0.643 AUTHOR 1EAH 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.
Cross-correlation coefficient REAL emd_50189_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 506.39996 506.39996 506.39996 90.0 90.0 90.0 X Y Z -0.30602738 1.0085871 0.004602094 0.07748959 1.055 1.055 1.055 AUTHOR emd_50189_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 0 0 0 480 480 480 506.39996 506.39996 506.39996 90.0 90.0 90.0 X Y Z -0.32801566 0.9589265 0.004604396 0.077605076 1.055 1.055 1.055 AUTHOR