2024-07-03 REL PDBj PDBj PDBj 2022-08-19 2022-10-26 2022-10-26 2024-07-03 Japan Society for the Promotion of Science (JSPS) Japan Japan Science and Technology Japan Complex structure of Clostridioides difficile binary toxin unfolded CDTa-bound CDTb-pore (short). Yamada T Kawamoto A Yoshida T Sato Y Kato T Tsuge H Complex, Translocation, Oligomer, Unfoldase, TOXIN Kawamoto A Yamada T Yoshida T Sato Y Kato T Tsuge H Cryo-EM structures of the translocational binary toxin complex CDTa-bound CDTb-pore from Clostridioides difficile. Nat Commun UK 13 6119 6119 2022 36253419 doi:10.1038/s41467-022-33888-4 2041-1723 EMD-32041 other EM volume EMD-32043 other EM volume EMD-33188 other EM volume EMD-34136 other EM volume 7yvs FULLOVERLAP Clostridioides difficile transferase complex Clostridioides difficile transferase complex 0 1 2 Clostridioides difficile ADP-ribosylating binary toxin binding subunit CdtB Clostridioides difficile 0.075657141 7 Escherichia coli BL21(DE3) LEVO NNNFFDPKLMSDWEDEDLDTDNDNIPDSYERNGYTIKDLIAVKWEDSFAEQGYKKYVSNYLESNTAGDPYTDYEKASGSF DKAIKTEARDPLVAAYPIVGVGMEKLIISTNEHASTDQGKTVSRATTNSKTESNTAGVSVNVGYQNGFTANVTTNYSHTT DNSTAVQDSNGESWNTGLSINKGESAYINANVRYYNTGTAPMYKVTPTTNLVLDGDTLSTIKAQENQIGNNLSPGDTYPK KGLSPLALNTMDQFSSRLIPINYDQLKKLDAGKQIKLETTQVSGNFGTKNSSGQIVTEGNSWSDYISQIDSISASIILDT ENESYERRVTAKNLQDPEDKTPELTIGEAIEKAFGATKKDGLLYFNDIPIDESCVELIFDDNTANKIKDSLKTLSDKKIY NVKLERGMNILIKTPTYFTNFDDYNNYPSTWSNVNTTNQDGLQGSANKLNGETKIKIPMSELKPYKRYVFSGYSKDPLTS NSIIVKIKAKEEKTDYLVPEQGYTKFSYEFETTEKDSSNIEITLIGSGTTYLDNLSITELNSTPEILDEPEVKIPTDQEI MDAHKIYFADLNFNPSTGNTYINGMYFAPTQTNKEALDYIQKYRVEATLQYSGFKDIGTKDKEMRNYLGDPNQPKTNYVN LRSYFTGGENIMTYKKLRIYAITPDDRELLVLSVD A8DS70 ADP-ribosylating binary toxin enzymatic subunit CdtA Clostridioides difficile 0.049420468999999995 1 Escherichia coli BL21(DE3) LEVO APIERPEDFLKDKEKAKEWERKEAERIEQKLERSEKEALESYKKDSVEISKYSQTRNYFYDYQIEANSREKEYKELRNAI SKNKIDKPMYVYYFESPEKFAFNKVIRTENQNEISLEKFNEFKETIQNKLFKQDGFKDISLYEPGKGDEKPTPLLMHLKL PRNTGMLPYTNTNNVSTLIEQGYSIKIDKIVRIVIDGKHYIKAEASVVSSLDFKDDVSKGDSWGKANYNDWSNKLTPNEL ADVNDYMRGGYTAINNYLISNGPVNNPNPELDSKITNIENALKREPIPTNLTVYRRSGPQEFGLTLTSPEYDFNKLENID AFKSKWEGQALSYPNFISTSIGSVNMSAFAKRKIVLRITIPKGSPGAYLSAIPGYAGEYEVLLNHGSKFKINKIDSYKDG TITKLIVDATLIPENLYFQGLEHHHHHH Q9KH42 CALCIUM ION 4.0078e-05 21 CA singleParticle particle 1.58 7.5
10 mM HEPES (pH 7.5), 1 mM CaCl2, and 0.003% (w/v) LMNG
 ETHANE 100 277 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 2.0 GATAN K3 (6k x 4k) 1 11284 3.36 50.0 1 735102 2.8 FSC 0.143 CUT-OFF cryoSPARC 100912 MAXIMUM LIKELIHOOD cryoSPARC 2 PROJECTION MATCHING emd_34137.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 380.16 380.16 380.16 90.0 90.0 90.0 X Y Z -0.71585613 1.5097827 0.00012184599 0.03744925 0.88 0.88 0.88 0.195 AUTHOR 7VNJ PDB experimental model emd_34137_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 380.16 380.16 380.16 90.0 90.0 90.0 X Y Z -0.16460429 0.67660433 0.000121845995 0.02076934 0.88 0.88 0.88 AUTHOR emd_34137_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 380.16 380.16 380.16 90.0 90.0 90.0 X Y Z -0.42771965 1.0148519 0.001109605 0.054598983 0.88 0.88 0.88 AUTHOR emd_34137_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 432 432 432 0 0 0 432 432 432 380.16 380.16 380.16 90.0 90.0 90.0 X Y Z -0.4590377 0.9614183 0.0010895553 0.054681297 0.88 0.88 0.88 AUTHOR