Feline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule A - leading to assembly of a portal structure at a unique three-fold axis.

2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DATABASE_REFERENCES citation _citation.journal_volume _citation.page_first _citation.page_last OTHER atom_sites _atom_sites.fract_transf_matrix[1][1] _atom_sites.fract_transf_matrix[2][2] _atom_sites.fract_transf_matrix[3][3] STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name PDBe PDBe 2018-06-14 2018-08-22 2019-01-16 2025-07-09 Medical Research Council (United Kingdom) MC_UU_12014/7 United Kingdom Biotechnology and Biological Sciences Research Council BB/J013854/1 United Kingdom Feline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule A - leading to assembly of a portal structure at a unique three-fold axis. Conley MJ Bhella D Capsid, Calicivirus, Vesivirus, Vp1, portal, Vp2, junctional-adhesion molecule A, VIRUS Conley MJ McElwee M Azmi L Gabrielsen M Byron O Goodfellow IG Bhella D Calicivirus VP2 forms a portal-like assembly following receptor engagement. Nature UK 565 377 381 2019 30626974 doi:10.1038/s41586-018-0852-1 1476-4687 0006 NATUAS EMD-0054 other EM volume

Icosahedral reconstruction of FCV strain F9

6gsi FULLOVERLAP Feline calicivirus strain F9 Feline calicivirus strain F9 0 1 2 3

Virus was propagated in Crandell Reese Feline Kidney cells

Felis catus Capsid 400.0 3 VIRION STRAIN false false Feline calicivirus strain F9 1 1

Icosahedral Capsid

Feline calicivirus strain F9 Felis catus Capsid 400.0 3 VIRION STRAIN false false feline junctional adhesion molecule A 1 2

Soluble ectodomain fragment comprising Ig-like domains D1 and D2

Felis catus VP2 - portal. 1 3

Postulated to mediate endosome escape, this virion component is only present on the outer surface of the capsid following receptor engagement.

Feline calicivirus strain F9 Capsid protein Feline calicivirus strain F9 0.073346664 4 LEVO MCSTCANVLKYYNWDPHFRLVIDPNKFLSVGFCDNPLMCCYPELLPEFGTVWDCDQSPLQIYLESILGDDEWASTYEAID PAVPPMHWDAAGKIFQPHPGVLMHHLIGEVAKAWDPNLPMFRLEADGDGSITAPEQGTPVGGVIAEPSAQMSAAADMATG KSVDSEWEAFFSFHTSVNWSTSETQGKILFKQSLGPLLNPYLEHLAKLYVAWSGSIDVRFSISGSGVFGGKLAAIVVPPG VDPVQSTSMLQYPHVLFDARQVEPVIFSIPDLRSTLYHLMSDTDTTSLVIMVYNDLINPYANDSNSSGCIVTVETKPGAD FKFHLLKPPGSMLTHGSVPSDLIPKSSSLWIGNRHWTDITDFVIRPFVFQANRHFDFNQETAGWSTPRYRPITITISEKN GAKLGIGVATDYIVPGIPDGWPDTTIPEKLTPAGDYAITNKSGNDITTAAGYDGADVIVNNTNFKGMYICGSLQRAWGDK KISNTAFITTATKVDNAIEPSNVIDMTKIAVYQDTHVGKEVQTSDDTLSLLGYTGIGEQAIGSDRDRVVRISVLPETGAR GGNHPIFYKNSIKLGYVIRSIDVFNSQILHTSRQLSLNHYLLPPDSFAVYRIIDSNGSWFDIGIDSDGFSFVGVSSIGKL EFPLTASYMGIQLAKIRLASNIRSSMTKL P27406 Junctional adhesion molecule A Felis catus 0.02218065 4 Cricetulus griseus LEVO AVYTSEPDVRVPEDKPAKLSCSYSGFSNPRVEWKFAHGDITSLVCYKNKITASYADRVTFSHSGITFHSVTRKDTGTYTC MVSDDGGNTYGEVSVQLTVLVPPSKPTVHIPSSATIGSRAVLTCSEKDGSPPSEYYWFKDGVRMPLEPKGNRAFSNSSYS LNEKTGELVFDPVSAWDTGEYTCEAQNGYGMPMRSEAVRMEA Q2WGK2 VP2 Feline calicivirus strain F9 0.012209837999999999 4 LEVO MNSILGLIDTVTNTIGKAQQIELDKAALGQQRELALKRMKLDHQALNNQVEQFNKILEQRVQGPIQSVRLARAAGFRVDP YSYTDQNFYDDQLNAIRLSYRNLFKN P28711 POTASSIUM ION 3.9098e-05 4 K singleParticle particle 1 7.2

Phosphate buffered saline

C-flat-2/2 COPPER 400 CARBON HOLEY ARRAY GLOW DISCHARGE 4 AIR ETHANE 100 277 FEI VITROBOT MARK IV

Purified virions were incubated in the presence of purified ectodomain fragments.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 1 13865 63.0

Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared

Images were motion-corrected using motioncor2 Defocus estimation was performed using GCTF

129884

Autopicking in Relion

Gctf

CTF correction was implemented through Relion

PHASE FLIPPING AND AMPLITUDE CORRECTION

Previously published models calculated at lower resolution.

C1 3.75 FSC 0.143 CUT-OFF RELION 2.1

Origins and orientations were originally assigned by 3D auto refinement with full icosahedral symmetry. Random group assignment was carried through the focussed classification process and used to divide the data into two roughly even halves that had been initially refined independently.

58510 PROJECTION MATCHING RELION 2.1 MAXIMUM LIKELIHOOD RELION 2.1 10 RELION 2.1

Origin and orientation values were initially determined by 3D auto refine in RELION, assuming full icosahedral symmetry (i.e. with full gold-standard methods). Once orientations were accurately determined relion_symmetry_expand was used to produce a STAR file with 60 orientations per particle. This was used for a focussed classification experiment in which a cylindrical mask was applied to a single three-fold axis for 3D classification without orientation refinement. One class showed the presence of the previously detected portal assembly. Particles contributed a median 3 views each. NOTE The reconstruction half-sets were calculated with C1 symmetry, however as three views per particle are present that are derived from icosahedral redundancy, C3 symmetry is imposed by the data.

emd_0056.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 -300 -300 -300 600 600 600 639.00006 639.00006 639.00006 90.0 90.0 90.0 X Y Z -0.11780139 0.21274377 0.00095921505 0.013303866 1.065 1.065 1.065 0.05 AUTHOR ::::EMDATABANK.org::::EMD-0056:::: C3 reconstruction of Feline Calicivirus decorated with a soluble ectodomain fragment of the cellular receptor feline junctional adhesion molecule A.