2024-07-10 REL PDBe PDBe PDBe 2024-05-23 2024-06-12 2024-06-12 2024-07-10 Wellcome Trust 224067/Z/21/Z United Kingdom Wellcome Trust 206377 United Kingdom Wellcome Trust 109363/Z/15/A United Kingdom Rhodobacter microvirus Ebor attached to B10 host cell reconstructed by single particle analysis with applied C5 symmetry Bardy P MacDonald CIW Jenkins HT Chechik M Hart SJ Turkenburg JP Blaza JN Fogg PCM Antson AA ssDNA virus, Microviridae, Tainavirinae, Alphaproteobacteria, Rhodobacter capsulatus, aquatic virus, jelly-roll fold, VIRUS Bardy P MacDonald CIW Kirchberger PC Jenkins HT Botka T Byrom L Alim NTB Traore DAK Konig HC Nicholas TR Chechik M Hart SJ Turkenburg JP Blaza JN Beatty JT Fogg PCM Antson AA A stargate mechanism of Microviridae genome delivery unveiled by cryogenic electron tomography. Biorxiv US 2024 38915634 doi:10.1101/2024.06.11.598214 2692-8205 EMD-50360 other EM volume
Native virion of Ebor attached to the outer membrane vesicle
 EMD-50361 other EM volume
Native virion of Ebor attached to the host cell reconstructed by subtomogram averaging
 EMD-50357 other EM volume
Native virion of Ebor, I4 symmetry
 EMD-50356 other EM volume
Empty virion of Ebor, I4 symmetry
 EMD-50358 other EM volume
In vitro-induced genome-releasing intermediate of Ebor, C5 symmetry
 Rhodobacter phage Ebor Rhodobacter phage Ebor 0 1
Phage, purified from Rhodobacter capsulatus strain SB1003 by ion-exchange chromatography, attached to host cell (B10 strain)
Rhodobacter phage Ebor variant R120 Rhodobacter capsulatus B10 5.7 Genome-releasing capsid 460.0 1 VIRION OTHER false false Major capsid protein Rhodobacter capsulatus SB 1003 SB1003 LEVO MSYQTKRNVRREARTLMGRFKAGKLAPVMAVPVKGSEGGMLSQSVSFELDPIAGRMATPITAEMCAVFVPVQACDALKNPEADYAGMTEIVREKLLSGNPLFVLEPETDVSKRCGVNPRRNNGLMRVNEIVRLAHNCAVNFLRRRRYVDAVQLTAANHSTTPAILSQTVLDRFNGALDPDPNVNGAVQLSMPDMRLPVASDAEKAVTAPLTVKRGNENRRLDAGISRLAAAEVAAATDAALYAVFGGREAGNVSLTDFYNAQKMDELTRVMRKICDDNPEYGEEMVLRWAHGLSVDPGRVPFLLAEKSVVLGRQIIGATDTAGVEDGVKRSDMAAQLSFTVPIPTTELGGIIVTFACIKPDETLSSQPHPILADHWRLDNFVADELALDPQPVMARELDYKVAQANETTVVFYTGLNELKKTYVSYGLCRALDPNTVESKNAVWQLEVPLSVTPETVLYPADLPQYPFADQQAEVCTYVVQSTAVMPTPMIFGPSPVEQLAVIETEDLFED singleParticle particle 7.75 20.0 Tris-HCl 100.0 NaCl sodium chloride 5.0 CaCl2 calcium chloride Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 100 295.15 FEI VITROBOT MARK IV
blot time 2 sec, blot force 0, wait time 8 sec.
concentration of 7x10^10 PFU/ml
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.75 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum GATAN K3 BIOQUANTUM (6k x 4k) 1 2750 27.9
acquired using lacey carbon setup in EPU
 1 75291
map of the native virus
 1 C5 FOURIER SPACE 7.84 FSC 0.143 CUT-OFF RELION 5
RELION skip align run, low passed filtered to the final estimated resolution using relion_image_handler
18179 MAXIMUM LIKELIHOOD RELION 5 MAXIMUM LIKELIHOOD RELION 5
icosahedral symmetry followed by symmetry expansion and classification in C5
 3 RELION 5
class 1 = 18179 particles, class 2 = 2741 particles, class 3 = 2175 particles
 emd_50359.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.015209306 0.023703791 0.00012116539 0.0032055227 2.143 2.143 2.143 0.004 AUTHOR Ebor attached to B10 host cell, class 1 emd_50359_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.016812896 0.023320312 0.0002447512 0.003472554 2.143 2.143 2.143 AUTHOR Ebor attached to B10 host cell, class 2 emd_50359_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.0116352895 0.023164067 0.0003369145 0.0032258292 2.143 2.143 2.143 AUTHOR Ebor attached to B10 host cell, class 3 emd_50359_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z 0.0 1.0 0.011461244 0.10336224 2.143 2.143 2.143 AUTHOR mask used for 3D classification emd_50359_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.052835044 0.06576568 0.000253832 0.00780924 2.143 2.143 2.143 AUTHOR half map 1 for class 2 emd_50359_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.07189739 0.07275085 0.00023277641 0.0077976184 2.143 2.143 2.143 AUTHOR half map 2 for class 2 emd_50359_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.062258165 0.08893353 0.00031745137 0.008619231 2.143 2.143 2.143 AUTHOR half map 1 for class 3 emd_50359_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.07440732 0.06513217 0.00035489563 0.008162436 2.143 2.143 2.143 AUTHOR half map 2 for class 3 emd_50359_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.025618726 0.03669196 0.00012314916 0.0041851425 2.143 2.143 2.143 AUTHOR half map 2 for class 1 emd_50359_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 548.608 548.608 548.608 90.0 90.0 90.0 X Y Z -0.02629875 0.03729218 0.00011891262 0.004197332 2.143 2.143 2.143 AUTHOR half map 1 for class 1