2024-07-10 REL PDBe PDBe PDBe 2020-05-29 2020-12-30 2020-12-30 2024-07-10 Bill & Melinda Gates Foundation RG.IMCB.I8-TSA-083 United Kingdom Poliovirus type 3 (strain Saukett) stabilised virus-like particle (PV3 SC8) from a mammalian expression system. Bahar MW Porta C Capsid protein, VIRUS LIKE PARTICLE Bahar MW Porta C Fox H Macadam AJ Fry EE Stuart DI Mammalian expression of virus-like particles as a proof of principle for next generation polio vaccines. NPJ Vaccines UK 6 5 5 2021 33420068 doi:10.1038/s41541-020-00267-3 2059-0105 6z6w FULLOVERLAP Human poliovirus 3 Human poliovirus 3 0 1 2 3
Recombinantly expressed virus-like particle of PV3 (strain Saukett).
Human poliovirus 3 Saukett Homo sapiens 5.85 Virus shell 1 310.0 1 VIRUS-LIKE PARTICLE SEROTYPE false true Capsid proteins, VP1 Human poliovirus 3 0.033562785000000005 1 mammal environmental sample LEVO GIEDLITEVAQGALTLSLPKQQDSLPDTKASGPAHSKEVPALTAVETGATNPLVPSDTVQTRHVIQRRSRSESTIESFFA RGACVAIIEVDNEEPTTRAQKLFAMWRITYKDTVQLRRKLEFFTYSRFDMELTFVVTANFTNTNNGHALNQVYQIMYIPP GAPTPKSWDDYTWQTSSNPSIFYTYGAAPARISVPYVGLANAYSHFYDGFAKVPLKTDANDQIGDSLYSAMTVDDFGVLA IRVVNDHNPTKVTSKVRIYMKPKHVRVWCPRPPRAVPYYGPGVDYKDNLNPLSEKGLTTY Q84895 Capsid proteins, VP0 Human poliovirus 3 0.037623023
Sequence is given for the VP0 polypeptide. Mutations are numbered according to sequence numbering for mature polypeptides VP2 and VP4.
1 mammal environmental sample LEVO MGAQVSSQKVGAHENSNRAYGGSTINYTTINYYKDSASNAASKQDYSQDPSKFTEPLKDVLIKTAPALNSPNVEACGYSD RVLQLTIGNSTITTQEAANSVVAYGRWPEFIRDDEANPVDQPTEPDVATCRFYTLDTVMWGKESKGWWWKLPDALRDMGL FGQNMYYHYLGRSGYTVHVQCNASKFHQGALGVFAIPEYCLAGDSDKQRYTSYANANPGEKGGKFYSQFNRDTAVTSPKR EFCPVDYLLGCGVLLGNAFVYPHQIINLRTNNSATIVLPYVNAMAIDSMVKHNNWGIAILPLSPLDFAQESSVEIPITVT IAPMCSEFNGLRNVTAPKFQ Q84895 Capsid proteins, VP3 Human poliovirus 3 0.026315099999999998 1 mammal environmental sample LEVO GLPVLNTPGSNQYLTSDNYQSPCAIPEFDVTPPIDIPGEVKNMMELAEIDTMIPLNLENTKRNTMDMYRVTLSDSADLSQ PILCFSLSPASDPRLSHTMLGEVLNYYTHWAGSLKFTFLFCGSMMATGKILVAYAPPGAQPPTSRKEAMLGTHVIWDLGL QSSCTMVVPWISNVTYRQTTQDSFTEGGYISMFYQTRIVVPLSTPKSMSMLGFVSACNDFSVRLLRDTTHISQSALPQ Q84895 SPHINGOSINE 0.000299492 1 SPH singleParticle particle 1.0 7.0 1.0 DPBS 20.0 EDTA
1 x DPBS, 20 mM EDTA, pH 7.0
 C-flat COPPER 400 CARBON LACEY 3.0 GLOW DISCHARGE AIR
The specific type of grid used was Ultra-thin carbon support film, 3nm - on lacey carbon AGS187-4 from Agar Scientific.
 ETHANE 100 277.15 FEI VITROBOT MARK IV
Double blotting with 4 ul of sample, followed by 4 second blot, before plunging..
Recombinantly expressed VLP of PV3.
 FEI POLARA 300 FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.5 3.5 160000.0 37037.0 GATAN LIQUID NITROGEN GIF Quantum LS 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 1-25 2 1465 5.0 40.0 1
Pixels size was 1.35 A/pixel
14021 EMD-3747
Startup model was low pass filtered to 60 Angstroms.
 1 I BACK PROJECTION 3.0 FSC 0.143 CUT-OFF RELION 3.1
Final reconstruction was sharpened with Post-processing in RELION using an inverse B-factor of -82.6 Angstroms.
9630 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 5 RELION 3.1 emd_11106.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 378.0 378.0 378.0 90.0 90.0 90.0 X Y Z -0.16487819 0.29022428 0.0041176737 0.022492874 1.35 1.35 1.35 0.07 AUTHOR MRC map filtered after local resolution in RELION. Recommended contour level 0.07 after inspection in Chimera. 5O5B PDB experimental model RIGID BODY FIT
Initial model was rigid body fitted using UCSF chimera, and the refined in real space using Phenix_real.space.refine.
Correlation coefficient REAL