2024-08-14 REL PDBe PDBe PDBe 2024-01-25 2024-06-19 2024-06-19 2024-08-14 Wellcome Trust 098302 United Kingdom Wellcome Trust 217089 United Kingdom Wellcome Trust 202679/Z/16/Z United Kingdom Wellcome Trust 206166/Z/17/Z United Kingdom Stalk-Arches-IMC at 4.33A - Refinement without symmetry of the Stalk-Arches-IMC from the fully-assembled R388 type IV secretion. Mace K Waksman G type IV secretion system type 4 secretion system T4SS Arches Stalk inner membrane complex IMC R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB3 VirB4 VirB5 VirB6 VirB8 VirB10 TrwM TrwK TrwJ TrwI TrwG TrwE, MEMBRANE PROTEIN Mace K Waksman G Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis. Embo J. UK 43 3287 3306 2024 38886579 doi:10.1038/s44318-024-00135-z 1460-2075 0897 EMJODG 8rtd FULLOVERLAP Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system Stalk-Arches-IMC complex from the fully-assembled R388 type IV secretion system 0 1 2 3 4 5 6 Escherichia coli TrwJ protein Escherichia coli 0.025190460999999997
Sequence from conjugative plasmid R388
5 Escherichia coli LEVO MKKLVMTAAVAAILGAASPVMAQGIPVFDGTRALDFVQQFARMKEQLDTAKDQLAEAQRMYEAVTGGRGLGDLMRNAQLR EYLPDDLRTVYDSANGGGYSGISGSINDILRDERLNGSVADMRRSIEERSRTAAATDKAVGLRAYEGAQQRLAQIEGLMD EISRTQDQKAIEELQARIAGEQAAIQNETTKLQMIAQLRQAEQALISEQRRERNMRILSSGNQGMPTIQ A8R752 TrwG protein Escherichia coli 0.025799993999999996
Sequence from conjugative plasmid R388
12 Escherichia coli LEVO MSKKQPKPVKAEQLKSYYEESRGLERDLIGEFVKSRKTAWRVATASGLFGLLGMVCGIVGFSQPAPAPLVLRVDNATGAV DVVTTLREHESSYGEVVDTYWLNQYVLNREAYDYNTIQMNYDTTALLSAPAVQQDYYKLFDGSNARDRVLGNKARITVRV RSIQPNGRGQATVRFTTQQHNSNGTVEAPQHQIATIGYTYIGAPMRSSDRLLNPLGFQVTSYRADPEILNN A8R756 TrwE protein Escherichia coli 0.042443785000000005
Sequence from conjugative plasmid R388
3 Escherichia coli LEVO MFGRKKGDVIDAGAELERAEQERIEGEYGASELASERRPHTPGARTLLMVLLCVIAVVLVTLSYKAYKVRGVVEDDDAQP QQVVRQVIPGYTPRPIRPEPENVPEPPQPTTSVPAIQPAPVTQPVRPQPTGPREKTPYELARERMLRSGLTAGSGGGEDL PRPQGGDVPAGGLMGGGGGGGELAEKLQPMRLSGSSAGRLGNRDMLITQGTQLDCVLETRLVTTQPGMTTCHLTRDVYST SGRVVLLDRGSKVVGFYQGGLRQGQARIFVQWSRIETPSGVVINLDSPGTGPLGEAGLGGWIDRHFWERFGGAIMISLIG DLGDWASRQGSRQGDNSIQFSNTANGVESAAAEALRNSINIPPTLYKNQGERVNILVARDLDFSDVYSLESIPTK A8R758 TrwI protein Escherichia coli 0.035324171999999994
Sequence from conjugative plasmid R388
5 Escherichia coli LEVO MAFELFTPLFNKIDQTTATYVTDISSRAIAAITPVVSVGLTLGFITYGWLIIRGAVEMPVAEFLNRCLRIGIIVSIALAG GLYQGEIANAITTVPDELASALLGNPTQGASAAALVDQSAQQGFDRASEAFEEAGFFSSDGLLYGLFGIIILLATGLLAA IGGAFLLLAKIALALLAGLGPLFILALIWQPTHRFFDQWAQQVLNYGLLIVLFAAVFGLLMQIFGSYMADLRFDGAQNVA YAIGGSVILSIVSIVLLMQLPSIASGLAGGIGLGYMWELRSMRSGAGAAMRGGRAMARGARAAPGAARGAAVGAANMAKT VATGGAGVARAAAGYFRGRKAG A8R754 TrwM protein Escherichia coli 0.012292584999999998
Sequence from conjugative plasmid R388
3 Escherichia coli LEVO MKPPQQQHEAFPLFKGATRLPTIWGVPMIPLMAMVMGVAVIALTVSIWWWALVPPLWFIMAQITKNDDKAFRIWWLWIDT KFRNRNKGFWGASSYSPANYRKRR A8R750 Type IV secretion system protein virB4 Escherichia coli 0.09376992999999999
Sequence from conjugative plasmid R388
6 Escherichia coli LEVO MGAIESRKLLASETPVGQFIPYSHHVTDTIISTKNAEYLSVWKIDGRSHQSASEADVFQWIRELNNTLRGISSANLSLWT HIVRRRVYEYPDAEFDNVFCRQLDEKYRESFTGYNLMVNDLYLTVVYRPVSDKVLSFFAKRERETPDQKKHRQESCIKAL EDINRTLGQSFKRYGAELLSVYEKGGHAFSAPLEFLARLVNGEHIPMPICRDRFSDYMAVNRPMFSKWGEVGELRSLTGL RRFGMLEIREYDDATEPGQLNVLLESDYEFVLTHSFSVLSRPAAKEYLQRHQKNLIDARDVATDQIEEIDEALNQLISGH FVMGEHHCTLTVYGETVQQVRDNLAHASAAMLDVAVLPKPVDLALEAGYWAQLPANWQWRPRPAPITSLNFLSFSPFHNF MSGKPTGNPWGPAVTILKTVSGTPLYFNFHASKEEEDATDKRLLGNTMLIGQSSSGKTVLLGFLLAQAQKFKPTIVAFDK DRGMEISIRAMGGRYLPLKTGEPSGFNPFQLPPTHANLIFLKQFVKKLAAAGGEVTHRDEEEIDQAITAMMSDSIDKSLR RLSLLLQFLPNPRSDDMDARPTVHARLVKWCEGGDYGWLFDNPTDALDLSTHQIYGFDITEFLDNPEARTPVMMYLLYRT ESMIDGRRFMYVFDEFWKPLQDEYFEDLAKNKQKTIRKQNGIFVFATQEPSDALESNIAKTLIQQCATYIFLANPKADYE DYTQGFKLTDSEFELVRGLGEFSRRFLIKQGDQSALAEMNLGKFRTIVDGETVERDFDDELLVLSGTPDNAEIAESIIAE VGDDPAVWLPIFLDRVKAERSDV A8R751 singleParticle particle 7.6 ETHANE TFS KRIOS OTHER OTHER FIELD EMISSION GUN 300 1.5 3.3000000000000003 GATAN K3 (6k x 4k) 57.5 1 4.33 FSC 0.143 CUT-OFF cryoSPARC 65173 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_19488.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -0.71761763 1.9973441 0.027171923 0.09129263 1.067 1.067 1.067 0.6 AUTHOR STALK-ARCHES-IMC _ Unsharpened emd_19488_msk_1.map emd_19488_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -0.0018734856 2.435959 0.0011052235 0.02346377 1.067 1.067 1.067 AUTHOR STALK-ARCHES-IMC _ Sharpened-deepEMhancer emd_19488_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -0.9710612 2.3075762 0.014889093 0.13737963 1.067 1.067 1.067 AUTHOR Half-A emd_19488_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 546.304 546.304 546.304 90.0 90.0 90.0 X Y Z -1.0162228 2.4174962 0.014896338 0.13734172 1.067 1.067 1.067 AUTHOR Half-B