Virion of native gene transfer agent (GTA) particle

2024-05-22 REL PDBe PDBe PDBe 2019-11-01 2020-07-22 2020-07-22 2024-05-22 Ministry of Education (MoE, Czech Republic) LQ1601 Czech Republic European Regional Development Fund CZ.1.05/1.1.00/02.0070 Czech Republic Ministry of Education (MoE, Czech Republic) LM2011033 Czech Republic Czech Science Foundation 15-21631Y Czech Republic Czech Science Foundation 18-17810S Czech Republic European Molecular Biology Organization (EMBO) 3041 Czech Republic Grant Agency of the Czech Republic 18-13064S Czech Republic Virion of native gene transfer agent (GTA) particle Bardy P Fuzik T "virion", "horizontal gene transfer", "gene delivery", "HK97", VIRUS Bardy P Fuzik T Hrebik D Pantucek R Thomas Beatty J Plevka P Structure and mechanism of DNA delivery of a gene transfer agent. Nat Commun UK 11 3034 3034 2020 32541663 doi:10.1038/s41467-020-16669-9 2041-1723 EMD-10442 other EM volume

capsid C5

EMD-10476 other EM volume

neck C12

EMD-10477 other EM volume

neck C6

EMD-10478 other EM volume

tail C6

EMD-10479 other EM volume

baseplate C6

EMD-10490 other EM volume

baseplate C3

EMD-10592 other EM volume

virion of empty GTA particle

6tba FULLOVERLAP Rhodobacter capsulatus DE442 Rhodobacter capsulatus SB 1003 0 1 2 3 4 5 6 7 8 9 10 11

phage-like particle mediating high-frequency horisontal gene transfer in Rhodobacterales species

Rhodobacter capsulatus SB 1003 Gene transfer agent Rhodobacter capsulatus 0.88 HK97-like oblate capsid 945.0 3 VIRION STRAIN false false Capsid 1 1 2 3

Oblate T=3 capsid

Rhodobacter capsulatus SB 1003 Gene transfer agent Head spike 1 2 3

penton protrusion of the capsid

Rhodobacter capsulatus SB 1003 Gene transfer agent Connector 1 4 5

special 5-fold vertex of the capsid, interconnecting capsid to tail

Rhodobacter capsulatus SB 1003 Gene transfer agent Tail 1 6 7 8 11

tubular structure interconnecting capsid to baseplate (host-recognition device)

Rhodobacter capsulatus SB 1003 Gene transfer agent Baseplate 1 9 10

host-recognition device present at the tip of the tail

Rhodobacter capsulatus SB 1003 Gene transfer agent Phage major capsid protein, HK97 family Rhodobacter capsulatus SB 1003 0.04089498799999999 145 LEVO MPEGADPVAEVKTALAGFLKEVKGFQDDVKTRLQQQEERVTMLQTKTYAGRHALAAAATEEAPHQKAFAAYLRTGDDDGL RGLSLEGKALNSAVAAEGGYLVDPQTSETIRGVLRSTASLRQIASVVNVEATSFDVLVDKTDMGSGWASETAALSETATP QIDRITIPLHELAAMPKASQRLLDDSAFDIETWLANRIADKFARAEAAAFISGDGVDKPTGFLTKTKVANGAWAWGSLGY VATGAAGDFAAVNASDAVVDLVYALGAEYRANASFVMNSKTAGAVRKMKDADGRFLWADSLAAGEPARLMGYPVLIAEDM PDIAANAYAIAFGDFGNGYTIAERPDLRVLRDPFSAKPHVLFYASKRVGGDVSDFAAIKLLKFAA D5ATZ3 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.009104348 55 LEVO MDVFAKHAVSLESPAVRHYEITPSDSTDLARRPRALRVQTGGTLVLRDETGITVTYTVFAGEILPVRPVRVLATGTTATA VGWE D5AR33 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.032996828 10 LEVO MIALGLGLGLAANGGPALRRYAVNGVAPVAVLDFERHFLSHPLALTRATSATYADALRAVQTAPADTPRYDYSTGKRALL LEASATNLLPNSAQFEAASWGKTRASVLANAALAPNGTMTADKLVEDTSNNSHFVARTGTQIAAGTSVTASIFVKAAERR WFALVTADSANAFRTTYFDLQTGTLGVVSQGAAGHVAQIVAAGNGWYRCSVTQTQAASGNFNFYPSVASANGATSYPGDG ASGLYLWGAQLEAGAAVSSVIPTEAAAVTRAADLASVAVAAGSYDLRRVDAAGTAVTKGVAHPGGALTIGAGSLYLLSLF PAGAL D5AR34 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.020956354 12 LEVO MMLNEVTAVPGTALPVAEFRDHLRLGTGFADLGAEDAALLSYLRAAIAAIEGRTAKALISRGFRLALTAWRWGDMQTLPI APVATVTALRLVDAAGVETPVAAGWRLVPDMARPRIEALGAMLPMIPTGGRVEIDFTAGFGASWSALPVDLAQAVFLLAA QYYELRHDGAAEGGAMPFGVMALIERWRTVRVLGGRP D5ATZ4 Portal protein Rcc01684 Rhodobacter capsulatus SB 1003 0.04284691 12 LEVO MGLNFFRKAAPEVRTEPVAERKASVTGRIVAMASGAGRPVWGPRDTVSLMRTGFAGNPVGFRSVKLIAEATAAVPLICQD AERRYEIHPVLDLLRRPNAGQGRAELFEALIGQILLSGNGYLEAVCPEPGVPRELHVLRSDRMAVVPGADGWPVGYDYTV GGRKHRFDMTGHPDPICHIKSFHPTDDHYGLSPMQAAAVALDVHNAASAWSKALLDNAARPSGAIIYKGADGQGVLAPEQ YERLIFEMETHHQGARNAGRPMLLEGGLDWKPMGFSPSDMEFHETKAAAAREIALAFGVPPMLIGIPGDATYANYAEANR AFYRLTVLPLLTRVSAALAWWLSGYLGAQIELKPDLDQVPALAVERDQLWARIGAAGFLSNSEKRVLLGLPPTAEG D5ATZ0 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.013871859 6 LEVO MSYAVAGALQAAVYQQLRADAVLAALVGTAVYDAVPPGPLAGTYVSLGPEDVADASDKTGAGAVHDFVISVITDAAGFAT AKAAAAAVSDALVGADLVLSRGRLVGLWFLRAKARRVEKADMRRIDLVFRARVEG D5ATZ6 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.012403122999999999 6 LEVO MSRPRLNRLLVLEEAVRVADGAGGHRLDWQAKGEVWAEVTAGSGSERAGEFVTLASVPFTIVVRAAPVGAARRPRPEQRF REGARIFRILAVAERDREGHYLSCFAREEVVA D5ATZ5 Phage major tail protein, TP901-1 family Rhodobacter capsulatus SB 1003 0.014420006999999999 30 LEVO MAAQNGKDLLIKLDLTGSGQFETIAGLRATRISFNAETVDVTSLESQGGWRELLGGAGVRSASISGAGVFKDADTDERAR QIFFDGEVPEFQVIIPDFGIVQGPFMITSIDYAGSHNGEASYELAMASAGALSFTAI D5ATZ7 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.031690734 3 LEVO MAYPESLKAHLQGGVTTLARAWALARADGRVLGFTDHDVVLRFDGISFEPGSGMTAKAVLQGTGLSVDNTESYGALSSEA ITEADLLAGRYDGAAVTVWLVNWADPAMRAVIFRGHLGEVSRGAGAFTAELRGLTAALGQEQGRIYHPRCAAVLGDGRCR FDLTKDGYALEAALGGVDEAVVLRLAEGAGFEDRWFEKGRLVVLDGAAAGLIGVVKNDRLQADGSRLIELWQRLGANPVA GDRVRIEPGCDKRAGTCRLKFDNFLNFRGFPHIPGEDWMVSYPVQSGTNDGGSLFR D5AU02 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.138527359 3 LEVO MATILLSAAGAAIGGGFGGTVLGLSGAVIGRAVGATLGRVIDQRLLGSGSQSVETGRVDRLRLSSASEGEAVGRLWGRMR VAGQVIWATRFFESASVEKSGKGVPRATVTSYSYSLSLALALCEGEILRVGRVWADGSEIEVSGLNMRVYRGGEDQLPDP KIAAVEGAEAAPAYRGIAYVVLEDLQLAPFGNRVPQFTFEVVRAAQGALAEAEPDLTRGLRAVALIPGTGEYALATTPVY LATGSGVTATQGVANQNAPGGQTDLVAALERLDEELPNCGAVSLVVSWFGDDLRCGACDVKPKVASVAEEGANMPWRVAG LERAGAEEVPRLSGQSVYGGTPADAAVIEAIAALRAAGKAVTFYPFILMAQLAGNGLPDPWNPGSAQPALPWRGRITLSV APGRAGSPDGTAAAEAQVAGFFGAASPGDSAIAGGEVVYSGPEEWSMRRFILHYAHLCQLAGGVDAFCIGTEMVALTQIR GPSNSFPAVAAFRQLAGEVKAILGPGCKIGYAADWSEYWGYAPGNGERFFHLDPLWADENIDFIGIDNYLPLSDWRDGAD HADAGWGSIHALDYLRSNIEGGEYYDWFYAAPEHRAAQIRTPITDGDHDEPWIWRAKDLRNWWLNDHHERVGGLRSEVAT AWVPQSKPIWFTEMGCAAIDKGTNQPNKFLDPKSSESGLPHHSDGRRDELIQMQYLRAMTGYWGEAARNPVSAVYGGPML DMSRAHVWAWDARPWPQFPLNTALWSDGENYARGHWISGRAVAQPLASVVAEICGAAGITEIDVSGLYGLVRGYTMTGDQ TGRAGLQALMLAYGFEALERDGQLVFRMRDGRVAADLAAADLALGEGEAVVETVRAAEAEIAGRVRLAYVEAEGDFEVKA VEAVFPDAAAGAAAGSELSLALTRAQAQGIVGRWLAEARVARDTARFALPPSRGHLGTGDVVRLDLPEGKRRYRIDRVEQ AGLIQVEAVRVEPGIYAPADEVEDPASLRPFAAPVPVTAVFLDLPLMKGDEDPVAPHLAVTATPWPGTVAVWSSDEDAGY ALNASLGTRAVIGQTLTPLFRARPGVWDRGAALRVRLASGALDSATAAKVLNGANAMAIGDGSSENWEVFQFAEAALVEG KIWDISLRLRGQLGTDALMPEVWPEGSVVVALNGAPEQILLPSAARGLARHYRIGAAVRSYDDPSFVHRIEAFAGAGLRP FSPCHLRAEPGASGWAFRWVRRTRIDGDSWQGYEVPLGETAELYLVRVLEGTAVKREVTVGEASWSYPAALQAADGIAGA FTLEVAQVSDVYGPGLAARITVGA D5AU04 Uncharacterized protein Rhodobacter capsulatus SB 1003 0.022985712999999998 6 LEVO MAFHEVRFPANLSFGSVGGPERRTEIVTLSSGHEERNSPWAHSRRHYDAGVGLRSLDDVERLIAFFEARGGQLHGFRWKD WADFKSCPASRAVAHEDQLIGMGDGVTTAFQLVKTYVSGGQSYLRPIVKPVEGTVKLGIAGDHQAEAVNFAVDHATGIVS FNEPPPQGARVTAGFEFDVPVRFDTDRIAVSVQSFQAGDLPQVPVVEVRI D5AU01 IRON/SULFUR CLUSTER 0.00035163999999999996 3 SF4 singleParticle particle 20 7.8 10.0 Tris 1.0 NaCl 1.0 MgCl2 1.0 CaCl2 0.01 Bovine serum albumin

G-buffer, doi: 10.1016/0003-9861(77)90508-2

Quantifoil R2/1 COPPER 300 CARBON HOLEY 11.0 GLOW DISCHARGE 30 OTHER ETHANE 100 293.15 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -1.0 -3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 42.75 1 53432

gradient descent method implemented in RELION

C1 BACK PROJECTION 4.54 FSC 0.143 CUT-OFF RELION 3.0

Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric reconstruction (EMD-10568) and tape-measure protein density from C3 reconstruction of tail tube (EMD-10570). Shown resoluton value corresponds to the map with lowest resolution (C3 tail tube).

27724 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_10443.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 960 960 960 0 0 0 960 960 960 1020.48 1020.48 1020.48 90.0 90.0 90.0 X Y Z 0.0 37.205703999999997 0.03369573 0.41731745 1.063 1.063 1.063 4.5 AUTHOR ::::EMDATABANK.org::::EMD-10443:::: virion of native GTA particle AB INITIO MODEL REAL