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 the host cell reconstructed by subtomogram averaging Bardy P Traore DAK Blaza JN Jenkins HT Nicholas TR Hart SJ Turkenburg JP Fogg PCM Antson AA ssDNA virus, Microviridae, Tainavirinae, Alphaproteobacteria, Rhodobacter capsulatus, aquatic virus, jelly-roll fold, in-toto, 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
Ebor native virion attached to the outer membrane vesicle
 EMD-50359 other EM volume
Ebor native virion attached to the host cell solved by single particle analysis
 EMD-50356 other EM volume
Empty virion of Ebor, I4 symmetry
 EMD-50357 other EM volume
Native 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
purified from Rhodobacter capsulatus strain SB1003 by ion-exchange chromatography
Rhodobacter phage Ebor Rhodobacter capsulatus B10 5.7 Native capsid 460.0 1 VIRION OTHER false false Major capsid protein Rhodobacter capsulatus SB 1003 SB1003 LEVO MSYQTKRNVRREARTLMGRFKAGKLAPVMAVPVKGSEGGMLSQSVSFELDPIAGRMATPITAEMCAVFVPVQACDALKNPEADYAGMTEIVREKLLSGNPLFVLEPETDVSKRCGVNPRRNNGLMRVNEIVRLAHNCAVNFLRRRRYVDAVQLTAANHSTTPAILSQTVLDRFNGALDPDPNVNGAVQLSMPDMRLPVASDAEKAVTAPLTVKRGNENRRLDAGISRLAAAEVAAATDAALYAVFGGREAGNVSLTDFYNAQKMDELTRVMRKICDDNPEYGEEMVLRWAHGLSVDPGRVPFLLAEKSVVLGRQIIGATDTAGVEDGVKRSDMAAQLSFTVPIPTTELGGIIVTFACIKPDETLSSQPHPILADHWRLDNFVADELALDPQPVMARELDYKVAQANETTVVFYTGLNELKKTYVSYGLCRALDPNTVESKNAVWQLEVPLSVTPETVLYPADLPQYPFADQQAEVCTYVVQSTAVMPTPMIFGPSPVEQLAVIETEDLFED subtomogramAveraging particle 6.8 30.0 DL-Malic acid 7.5 (NH4)2SO4 ammonium sulphate 5.1 K2HPO4 Dipotassium phosphate 4.5 KH2PO4 Monopotassium phosphate 1.0 Supersalt solution 4.0 O-Acetylserine
minimal RCV media for growing Rhodobacter, reference 10.1016/0003-9861(61)90073-x
 Quantifoil R2/1 COPPER 200 CARBON HOLEY GLOW DISCHARGE AIR 0.026000000000000002 NITROGEN 60 FEI VITROBOT MARK IV
single side blotting, 9 sec blotting time, 2 sec wait time, 0 force, 0 drain time.
phage Ebor mixed with cells of R. capsulatus B10 strain in titre of 7x10^10 PFU/ml
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 1.5 4.0 49000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris 10
instrument TFS Glacios 2
FEI FALCON IV (4k x 4k) 1 1.33 3.18
Direct electron detector model is TFS Falcon 4(i)
 1 C1 31.0 OTHER EMAN2
FSC 0.2 CUT-OFF
1556 27 1593 native map of Ebor derived from SPA template matching EMAN2
template matching was performed using EMAN2 with a reference map of Ebor generated from single particle analysis, manual deletion of bad particles
 3 EMAN2
class 1 = 285 particles, class 2 = 191 particles, class 3 = 110 particles; classification done in C5
 PROJECTION MATCHING EMAN2 emd_50361.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 -180 -180 -180 360 360 360 900.0 900.0 900.0 90.0 90.0 90.0 X Y Z -7.195881 11.182119 0.31384975 1.0001552 2.5 2.5 2.5 2.6 AUTHOR C1 reconstruction of Ebor virion attached to the host cell emd_50361_msk_1.map emd_50361_additional_7.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -2.3425405 3.6081848 0.13606685 0.6579428 5.0 5.0 5.0 AUTHOR C5 classification, class 2 filtered emd_50361_additional_6.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -2.6778612 3.896819 0.13606684 0.6573878 5.0 5.0 5.0 AUTHOR C5 classification, class 1 filtered emd_50361_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -3.0629907 3.4164214 0.13606685 0.6582511 5.0 5.0 5.0 AUTHOR C5 classification, class 3 filtered emd_50361_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -5.7007766 9.483986 0.13606685 0.97469795 5.0 5.0 5.0 AUTHOR C5 reconstruction of Ebor virion attached to the host cell emd_50361_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -2.4555666 3.1236699 0.09919435 0.9999998 5.0 5.0 5.0 AUTHOR C5 classification, class 3 unfiltered emd_50361_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -1.8943084 2.981081 0.07557026 0.99999976 5.0 5.0 5.0 AUTHOR C5 classification, class 2 unfiltered emd_50361_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 128 128 128 -64 -64 -64 128 128 128 640.0 640.0 640.0 90.0 90.0 90.0 X Y Z -1.9106421 3.0257983 0.07350218 0.9999998 5.0 5.0 5.0 AUTHOR C5 classification, class 1 unfiltered emd_50361_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 -180 -180 -180 360 360 360 900.0 900.0 900.0 90.0 90.0 90.0 X Y Z -0.009698534 0.009875393 0.000049088267 0.0022231168 2.5 2.5 2.5 AUTHOR emd_50361_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 -180 -180 -180 360 360 360 900.0 900.0 900.0 90.0 90.0 90.0 X Y Z -0.009789764 0.009968287 0.0000468913 0.0022457407 2.5 2.5 2.5 AUTHOR