2024-11-06 REL PDBe PDBe PDBe 2018-06-20 2018-07-18 2018-11-21 2024-11-06 Academy of Finland 275199 Finland European Union PIEF-GA-2013-628150 European Union PIAPP-GA-2013-612308 European Union 653706 High-resolution Cryo-EM of Fab-labeled human parechovirus 3 Domanska A Flatt JW human parechovirus, antibody, RNA, VIRUS Domanska A Flatt JW Jukonen JJJ Geraets JA Butcher SJ A 2.8-Angstrom-Resolution Cryo-Electron Microscopy Structure of Human Parechovirus 3 in Complex with Fab from a Neutralizing Antibody. J.Virol. US 93 2019 30463974 doi:10.1128/JVI.01597-18 1098-5514 0825 JOVIAM 6gv4 FULLOVERLAP Human parechovirus type 3 in complex with fabs from AT12-015 Human parechovirus type 3 in complex with fabs from AT12-015 0 1 2 3 4 5 6 7.7 Human parechovirus 3 1 1 2 3 4 Human parechovirus 3 A308/99 VIRION STRAIN false false fabs from AT12-015 1 5 6 Homo sapiens RNA (5'-R(*UP*GP*GP*UP*AP*UP*UP*U)-3') Human parechovirus 3 colon adenocarcinoma 0.002505489
RNA
1 UGGUAUUU VP0 Human parechovirus 3 colon adenocarcinoma 0.031770135 1 LEVO MESIKDLVNVATGAMDTLSLSNVETEVNNIISGNEVGGEIITKVADDASNLLGPNSFATTAQPENKDVVQATTTVNTTNL TQHPSAPTIPFTPDFKNVDNFHSMAYDITTGDKNPSKLIRLDTASWQTSYSRQYEITTVELPKSFWDDTRKPAYGQAKYF AAVRCGFHFQVQVNVNQGTAGSALVVYEPKPVIDSRQYLEFGSLTNLPHVLMNLAETTQADLCIPYVADTNYVKTDSSDL GQLRVYVWTPLSVPTGASNEVDVTVMGSLLQLDFQNPRPYGEDVEIYDN Q8BES5 VP1 Human parechovirus 3 colon adenocarcinoma 0.025913126999999998 1 LEVO NSWGSQMDLTDPLCIEDNMENCKQSISPNELGLTSAQDDGPLGNEKPNYFLNFRTMNVDIFTVSHTKVDNIFGRAWYVTS HDFNNGDTWRQKLTFPKEGHGMLSQFFAYFTGEINIHILYMAKQGFLRVAHTYDTEDNRKTFLSSNGVITIPAGEQMTLS VPFYSNKPLRTVRHDSALGFLMCRPSMHGTTRTTVEVYVSLRCPNFFFPVPAPKPTGSRATALSDESPY Q8BES5 VP3 Human parechovirus 3 colon adenocarcinoma 0.028757551
polypeptide chain
1 LEVO GPNKANVSKFNKRKFLTASTKYKWTRTKVDIAEGPGTMNMANVLSTTGAQSVALVGERAFYDPRTAGSKSRFDDMIKIAQ LFSVMSDNTTPSSSSGIDKYGYFDWAATVAPQNMVHRNVVTLDQFPNLNLFMNTYSYFRGSLIIRLSIYASTFNRGRLRM GFFPNCTHDTQLELDNAIYTICDIGSDNSFELTIPYSFSTWMRKTHGHQLGLFQVEVLNRLTYNSSSPNKVHCIVQGRLG DDAKFFCPTGSLVSFQ Q8BES5 AT12-015 antibody variable heavy Homo sapiens 0.013128612999999999
polypeptide chain
1 Homo sapiens LEVO EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGGGDSRYYADSVKGRFTISRDNSKNTLY LQMNSLGAEDTALYYCAKRLGRVAEYYFDYWGQGTLVTVSP AT12-015 antibody variable light Homo sapiens 0.012339752
polypeptide chain
1 Homo sapiens LEVO DIQMTQSPSTLSASVGDRVTITCRTSQSISNWLAWYQQKPGKAPKLLIYQASTLENGVPSRFTGSGSGTEFSLTISSLQP DDFATYYCQQYNNYMALTFGGGTKVEIKRTVAA singleParticle particle 0.1 7.5 10.0 Tris-HCl tris hydrochloride 150.0 NaCl sodium chloride 1.0 MgCL magnesium chloride COPPER 400 CARBON LACEY GLOW DISCHARGE
ultrathin carbon-coated lacey 400-mesh copper grids (Ted Pella product #01824)
 ETHANE 295 HOMEMADE PLUNGER
We could not control humidity during plunging. It was ambient humidity. Blot for 1 s before plunging..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.5 2.5 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON II (4k x 4k) INTEGRATING 2-17 2 6541 1.0 48.0 1 217212
automatic particle selection in RELION using template generated from manually selected particles
Low resolution cryo-EM map done in AUTO3DEM from images of the same sample taken with FEI Tecnai TF20 on CCD camera
 3 I 2.8 FSC 0.143 CUT-OFF RELION 2.1 74927 ANGULAR RECONSTITUTION RELION 2.0 MAXIMUM LIKELIHOOD RELION 2.0 10 RELION 2.1 emd_0069.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 480 480 480 -240 -240 -240 480 480 480 508.8 508.8 508.8 90.0 90.0 90.0 X Y Z -0.19998817 0.41895282 0.0015927622 0.024973061 1.06 1.06 1.06 0.05 AUTHOR Human parechovirus type 3 in complex with neutralizing human monoclonal antibody Fabs Post-processed map, B factor -70 OTHER
Initial model was generated in I-TASSER and SWISSMODEL using 4z92 and 4udf as reference. Initial rigid fit of the model to the map was done in UCSF Chimera. Model refinement was done in Coot and MDFF.
REAL