2024-10-23 REL PDBe PDBe PDBe 2024-05-24 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 compound 18 (CL304) 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:10.1002/pro.3943 0961-8368 0795 PRCIEI 9fgn 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 0.031952896 1 LEVO GDVEEAIERAVVHVADTMRSGPSNSASVPALTAVETGHTSQVTPSDTMQTRHVKNYHSRSESTVENFLGRSACVYMEEYK TTDNDVNKKFVAWPINTKQMVQMRRKLEMFTYLRFDMEVTFVITSRQDPGTTLAQDMPVLTHQIMYVPPGGPIPAKVDDY AWQTSTNPSIFWTEGNAPARMSIPFISIGNAYSNFYDGWSNFDQRGSYGYNTLNNLGHIYVRHVSGSSPHPITSTIRVYF KPKHTRAWVPRPPRLCQYKKAFSVDFTPTPITDTRKDINTVT P21404 Capsid protein VP2 Coxsackievirus A9 Griggs kidney 0.027720284999999997 1 LEVO SDRVRSITLGNSTITTQECANVVVGYGRWPTYLRDDEATAEDQPTQPDVATCRFYTLDSIKWEKGSVGWWWKFPEALSDM GLFGQNMQYHYLGRAGYTIHVQCNASKFHQGCLLVVCVPEAEMGGAVVGQAFSATAMANGDKAYEFTSATQSDQTKVQTA IHNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHYNFTLMVIPFVKLDYADTASTYVPITVTVAPMC AEYNGLRLAQ P21404 Capsid protein VP3 Coxsackievirus A9 Griggs kidney 0.026149889 1 LEVO LPTMNTPGSTQFLTSDDFQSPCALPQFDVTPSMNIPGEVKNLMEIAEVDSVVPVNNVQDTTDQMEMFRIPVTINAPLQQQ VFGLRLQPGLDSVFKHTLLGEILNYYAHWSGSMKLTFVFCGSAMATGKFLIAYSPPGANPPKTRKDAMLGTHIIWDIGLQ SSCVLCVPWISQTHYRLVQQDEYTSAGYVTCWYQTGMIVPPGTPNSSSIMCFASACNDFSVRMLRDTPFISQDNKL P21404 Capsid protein VP4 Coxsackievirus A9 Griggs kidney 0.0072379359999999995 1 LEVO GAQVSTQKTGAHETSLSAAGNSIIHYTNINYYKDAASNSANRQDFTQDPSKFTEPVKDVMIKSLPAL P21404 ~{N}-[[2,4-bis(fluoranyl)phenyl]methyl]-4-[(4-methylpiperazin-1-yl)methyl]aniline 0.000331403 1 A1ICH singleParticle particle 0.4 7.2
PBS containing 2 mM MgCl2 and 5% DMSO.
 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..
Compound 18 (CL304) was solubilized in DMSO and diluted to the final concentration in PBS + 2 mM MgCl2. Purified Coxsackievirus A9 was incubated with compound 18 (CL304) for 1h at 37C after which the sample was vitrified on a semi-automatic plunger Leica EM GP on copper Quantifoil R1.2/1.3 grids with 2 nm thin carbon film and 300 mesh. This sample was monodisperse.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.6 2.3000000000000003 150000.0 NITROGEN 93.15 103.15 FEI FALCON III (4k x 4k) COUNTING 1496 1496 625 1.0 40.0 1 26019
Initial model was generated in cryoSPARC utilising Ab Initio model protocol.
 I FOURIER SPACE 2.64 FSC 0.143 CUT-OFF cryoSPARC 4.3.0 Non-uniform refinement job in cryoSPARC was used for final reconstruction angle assignment 22815 MAXIMUM LIKELIHOOD cryoSPARC 4.3.0 Protocol for Ab Initio implemented in cryoSPARC was used for model creation MAXIMUM LIKELIHOOD cryoSPARC 4.3.0 cryoSPARC 4.3.0 Heterogeneous refinement implemented in cryoSPARC was used for 3D classification emd_50414.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 436.5 436.5 436.5 90.0 90.0 90.0 X Y Z -0.5334008 1.3570522 0.026393361 0.12541772 0.97 0.97 0.97 0.21 AUTHOR Flipped-handedness map of Coxsackievirus A9 bound to CL304 (compound 18) resolved to 2.6 A. 8AT5 PDB experimental model 132.099999999999994 emd_50414_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 436.5 436.5 436.5 90.0 90.0 90.0 X Y Z -0.62350017 1.3431212 0.010106519 0.1303664 0.97 0.97 0.97 AUTHOR Half-map of Coxsackievirus A9 bound to CL304 (compound 18). emd_50414_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 450 450 450 0 0 0 450 450 450 436.5 436.5 436.5 90.0 90.0 90.0 X Y Z -0.5218025 1.3514379 0.010108253 0.13025844 0.97 0.97 0.97 AUTHOR Half-map of Coxsackievirus A9 bound to CL304 (compound 18)