2024-10-23 REL PDBe PDBe PDBe 2024-06-13 2024-10-02 2024-10-02 2024-10-23 Academy of Finland 315950 Finland Sigrid Juselius Foundation 95-7202-38 Finland Jane and Aatos Erkko Foundation Finland Coxsackievirus A9 bound with CL213. Plavec Z Butcher SJ Mitchell C Buckner C Antiviral, capsid stabilizer, hydrophobic pocket, cryoEM, VIRUS Tammaro C Plavec Z Myllymaki L Mitchell C Consalvi S Biava M Ciogli A Domanska A Leppilampi V Buckner C Manetto S Scio P Coluccia A Laajala M Dondio GM Bigogno C Marjomaki V Butcher SJ Poce G SAR Analysis of Novel Coxsackie virus A9 Capsid Binders. J.Med.Chem. US 67 17144 17161 2024 39292620 doi:10.1021/acs.jmedchem.4c00701 0022-2623 0151 JMCMAR Pettersen EF Goddard TD Huang CC Meng EC Couch GS Croll TI Morris JH Ferrin TE UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Sci US 30 70 82 2021 32881101 doi:10.7554/eLife.53740 1469-896X 0795 PRCIEI 9fp5 FULLOVERLAP Human coxsackievirus A9 (strain Griggs) Human coxsackievirus A9 (strain Griggs) 0 1 2 3 4
Coxsackievirus A9 was propagated on green monkey kidney cells and purified on a sucrose gradient.
Human coxsackievirus A9 (strain Griggs) Griggs Homo sapiens 8 icosahedral capsid 300.0 1 VIRION STRAIN false false Capsid protein VP1 Coxsackievirus A9 Griggs kidney 0.03386901999999999 1 LEVO GDVEEAIERAVVHVADTMRSGPSNSASVPALTAVETGHTSQVTPSDTMQTRHVKNYHSRSESTVENFLGRSACVYMEEYK TTDNDVNKKFVAWPINTKQMVQMRRKLEMFTYLRFDMEVTFVITSRQDPGTTLAQDMPVLTHQIMYVPPGGPIPAKVDDY AWQTSTNPSIFWTEGNAPARMSIPFISIGNAYSNFYDGWSNFDQRGSYGYNTLNNLGHIYVRHVSGSSPHPITSTIRVYF KPKHTRAWVPRPPRLCQYKKAFSVDFTPTPITDTRKDINTVTTVAQSRRRGDMSTLNTH P21404 Capsid protein VP2 Coxsackievirus A9 Griggs kidney 0.028885518 1 LEVO SPTVEECGYSDRVRSITLGNSTITTQECANVVVGYGRWPTYLRDDEATAEDQPTQPDVATCRFYTLDSIKWEKGSVGWWW KFPEALSDMGLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGGAVVGQAFSATAMANGDKAYEFTSATQ SDQTKVQTAIHNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHYNFTLMVIPFVKLDYADTASTYVP ITVTVAPMCAEYNGLRLAQAQ P21404 Capsid protein VP3 Coxsackievirus A9 Griggs kidney 0.026335071999999998 1 LEVO GLPTMNTPGSTQFLTSDDFQSPCALPQFDVTPSMNIPGEVKNLMEIAEVDSVVPVNNVQDTTDQMEMFRIPVTINAPLQQ QVFGLRLQPGLDSVFKHTLLGEILNYYAHWSGSMKLTFVFCGSAMATGKFLIAYSPPGANPPKTRKDAMLGTHIIWDIGL QSSCVLCVPWISQTHYRLVQQDEYTSAGYVTCWYQTGMIVPPGTPNSSSIMCFASACNDFSVRMLRDTPFISQDNKLQ P21404 Capsid protein VP4 Coxsackievirus A9 Griggs kidney 0.0073520389999999994 1 LEVO GAQVSTQKTGAHETSLSAAGNSIIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDVMIKSLPALN P21404 PALMITIC ACID 0.00025642399999999994 1 PLM MYRISTIC ACID 0.000228371 1 MYR singleParticle particle 0.07 7.2 Quantifoil R1.2/1.3 COPPER 300 CARBON CONTINUOUS 2.0 GLOW DISCHARGE ETHANE 80 295 LEICA EM GP
Sample was incubated for 15 s on the grid before blotted from the front for 1.5 s..
CL213 stock solution in DMSO was diluted in PBS containing 2mM MgCl2 for final concentration of 1 mg/ml. 10 ul of purified CVA9 with the concentration of 0.7 mg/ml was mixed with 4 ul of CL213 diluted in PBS containing 2mM MgCl2 to a final concentration of CL213 of 0.28 mg/ml. The virus-compound mixture was incubated for 1 hour in 37 C. The final molar concentration of the virus was approximately 71 nM and CL213 concentration was approximately 7.8 mM.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 2.0 GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 216957
The initial reference free 3-dimensional (3D) model was done using RELION- 3D Initial Model protocol with 3.7 degrees of angular sampling using 118 374 particles.
 I 2.5 FSC 0.143 CUT-OFF Scipion 3.0.8 90678 MAXIMUM LIKELIHOOD Scipion 3.0.8 MAXIMUM LIKELIHOOD Scipion 3.0.8 Scipion 3.0.8 One high quality class containing 90 678 well- resolved particles was chosen for further analysis. emd_50636.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.008171182 0.018075097 0.00024631157 0.0016956831 1.08 1.08 1.08 0.0036 AUTHOR Map of Coxsackievirus A9 bound to CL213 at a resolution of 2.5 A. 8AT5 PDB experimental model 70.0 emd_50636_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.008544125 0.018685779 0.00024643648 0.001728869 1.08 1.08 1.08 AUTHOR Half-map of Coxsackievirus A9 bound to CL213. emd_50636_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 432.00003 432.00003 432.00003 90.0 90.0 90.0 X Y Z -0.008845798 0.018918352 0.00024802715 0.0017273865 1.08 1.08 1.08 AUTHOR Half-map of Coxsackievirus A9 bound to CL213.