Baseplate of native GTA particle computed with C3 symmetry

2024-05-22 REL PDBe PDBe PDBe 2019-11-12 2019-12-25 2020-07-22 2024-05-22 Ministry of Education (Czech Republic) LQ1601 Czech Republic European Regional Development Fund CZ.1.05/1.1.00/02.0070 Czech Republic Ministry of Education (Czech Republic) LM2011033 Czech Republic Czech Science Foundation 15-21631Y Czech Republic Czech Science Foundation 18-17810S Czech Republic European Molecular Biology Organization 3041 Czech Republic Grant Agency of the Czech Republic 18-13064S Czech Republic Baseplate of native GTA particle computed with C3 symmetry Bardy P Fuzik T "baseplate", "tail", "oligosaccharide-binding fold", "hub", 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-10443 other EM volume

virion of native GTA particle

EMD-10479 other EM volume

tail-baseplate interface of native GTA particle computed with C6 symmetry

6teh FULLOVERLAP Rhodobacter capsulatus DE442 gene transfer agent baseplate Rhodobacter capsulatus DE442 gene transfer agent baseplate 0 1 2 3

host recognition device present at the tip of the tail

Rhodobacter capsulatus DE442 1.00 Putative gene transfer agent protein Rhodobacter capsulatus 0.031690734 1 LEVO MAYPESLKAHLQGGVTTLARAWALARADGRVLGFTDHDVVLRFDGISFEPGSGMTAKAVLQGTGLSVDNTESYGALSSEA ITEADLLAGRYDGAAVTVWLVNWADPAMRAVIFRGHLGEVSRGAGAFTAELRGLTAALGQEQGRIYHPRCAAVLGDGRCR FDLTKDGYALEAALGGVDEAVVLRLAEGAGFEDRWFEKGRLVVLDGAAAGLIGVVKNDRLQADGSRLIELWQRLGANPVA GDRVRIEPGCDKRAGTCRLKFDNFLNFRGFPHIPGEDWMVSYPVQSGTNDGGSLFR A0A9U0 Putative gene transfer agent protein Rhodobacter capsulatus 0.138527359 1 LEVO MATILLSAAGAAIGGGFGGTVLGLSGAVIGRAVGATLGRVIDQRLLGSGSQSVETGRVDRLRLSSASEGEAVGRLWGRMR VAGQVIWATRFFESASVEKSGKGVPRATVTSYSYSLSLALALCEGEILRVGRVWADGSEIEVSGLNMRVYRGGEDQLPDP KIAAVEGAEAAPAYRGIAYVVLEDLQLAPFGNRVPQFTFEVVRAAQGALAEAEPDLTRGLRAVALIPGTGEYALATTPVY LATGSGVTATQGVANQNAPGGQTDLVAALERLDEELPNCGAVSLVVSWFGDDLRCGACDVKPKVASVAEEGANMPWRVAG LERAGAEEVPRLSGQSVYGGTPADAAVIEAIAALRAAGKAVTFYPFILMAQLAGNGLPDPWNPGSAQPALPWRGRITLSV APGRAGSPDGTAAAEAQVAGFFGAASPGDSAIAGGEVVYSGPEEWSMRRFILHYAHLCQLAGGVDAFCIGTEMVALTQIR GPSNSFPAVAAFRQLAGEVKAILGPGCKIGYAADWSEYWGYAPGNGERFFHLDPLWADENIDFIGIDNYLPLSDWRDGAD HADAGWGSIHALDYLRSNIEGGEYYDWFYAAPEHRAAQIRTPITDGDHDEPWIWRAKDLRNWWLNDHHERVGGLRSEVAT AWVPQSKPIWFTEMGCAAIDKGTNQPNKFLDPKSSESGLPHHSDGRRDELIQMQYLRAMTGYWGEAARNPVSAVYGGPML DMSRAHVWAWDARPWPQFPLNTALWSDGENYARGHWISGRAVAQPLASVVAEICGAAGITEIDVSGLYGLVRGYTMTGDQ TGRAGLQALMLAYGFEALERDGQLVFRMRDGRVAADLAAADLALGEGEAVVETVRAAEAEIAGRVRLAYVEAEGDFEVKA VEAVFPDAAAGAAAGSELSLALTRAQAQGIVGRWLAEARVARDTARFALPPSRGHLGTGDVVRLDLPEGKRRYRIDRVEQ AGLIQVEAVRVEPGIYAPADEVEDPASLRPFAAPVPVTAVFLDLPLMKGDEDPVAPHLAVTATPWPGTVAVWSSDEDAGY ALNASLGTRAVIGQTLTPLFRARPGVWDRGAALRVRLASGALDSATAAKVLNGANAMAIGDGSSENWEVFQFAEAALVEG KIWDISLRLRGQLGTDALMPEVWPEGSVVVALNGAPEQILLPSAARGLARHYRIGAAVRSYDDPSFVHRIEAFAGAGLRP FSPCHLRAEPGASGWAFRWVRRTRIDGDSWQGYEVPLGETAELYLVRVLEGTAVKREVTVGEASWSYPAALQAADGIAGA FTLEVAQVSDVYGPGLAARITVGA A0A9S9 Putative gene transfer agent protein Rhodobacter capsulatus 0.022985712999999998 2 LEVO MAFHEVRFPANLSFGSVGGPERRTEIVTLSSGHEERNSPWAHSRRHYDAGVGLRSLDDVERLIAFFEARGGQLHGFRWKD WADFKSCPASRAVAHEDQLIGMGDGVTTAFQLVKTYVSGGQSYLRPIVKPVEGTVKLGIAGDHQAEAVNFAVDHATGIVS FNEPPPQGARVTAGFEFDVPVRFDTDRIAVSVQSFQAGDLPQVPVVEVRI A0A9T9 IRON/SULFUR CLUSTER 0.00035163999999999996 1 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 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 1 3114 1.0 42.75 1 42242 stochastic gradient descent in RELION 2.1 de novo C3 BACK PROJECTION 3.99 FSC 0.143 CUT-OFF RELION 3.0 42242 MAXIMUM LIKELIHOOD RELION 2.1 MAXIMUM LIKELIHOOD RELION 3.0 emd_10490.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 318.9 318.9 318.9 90.0 90.0 90.0 X Y Z -0.057781424 0.20532729 0.0006629171 0.0048486223 1.063 1.063 1.063 0.0268 AUTHOR ::::EMDATABANK.org::::EMD-10490:::: baseplate of native GTA particle, C3 symmetrized AB INITIO MODEL REAL