2026-03-11 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY RCSB RCSB 2025-05-04 2026-03-11 2026-03-11 2026-03-11 The Hospital For Sick Children Foundation Canada CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with taurochenodeoxycholic acid (TCDCA) Miletic S Li Z Melnyk RA clostridioides difficile, Toxin B, TcdB, Bile acid, TCDCA, TOXIN Miletic S Icho S Li Z Tam J Rose EC Perkins CE Nakhi A Yang X Hang HC Rubinstein JL Dosa PI Theriot CM Melnyk RA Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin. Nat Microbiol UK 10 3215 3228 2025 41254394 doi:10.1038/s41564-025-02179-1 2058-5276 EMD-70487 other EM volume
CryoEM structure of Toxin B (TcdB) from Clostridioides difficile complexed with methyl cholate (CA-Methyl)
 EMD-70488 other EM volume
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the closed CROP state
 EMD-70489 other EM volume
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the open CROP state
 9ohc FULLOVERLAP EMDB EMD-70486 associated EM volume
CryoEM structure of Toxin B (TcdB) from clostridioides difficile complexed with taurochenodeoxycholic acid (TCDCA)
 EMDB EMD-70487 other EM volume
CryoEM structure of Toxin B (TcdB) from Clostridioides difficile complexed with methyl cholate (CA-Methyl)
 EMDB EMD-70488 other EM volume
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the closed CROP state
 EMDB EMD-70489 other EM volume
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the open CROP state
 PDB 9OHD unspecified
CryoEM structure of Toxin B (TcdB) from Clostridioides difficile complexed with methyl cholate (CA-Methyl)
 PDB 9OHE unspecified
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the closed CROP state
 PDB 9OHF unspecified
CryoEM structure of apo Toxin B (TcdB) from Clostridioides difficile in the open CROP state
 Clostridioides difficile Toxin B (TcdB) complexed with the natural bile acid TCDCA Clostridioides difficile Toxin B (TcdB) complexed with the natural bile acid TCDCA 0 1
500 micromolar TCDCA
Clostridioides difficile VPI 10463 0.276 Toxin B Clostridioides difficile VPI 10463 0.270767281 1 Priestia megaterium LEVO MSLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKALKKFKEYLV TEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAINDTLESFREN LNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDV RNFEEFKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESIEKPSSVTVDFWEMTKLEAI MKYKEYIPEYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIV KQIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQD LLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSLGEDDNLDFSQNIVVDKE YLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSII SDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVK DKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNLPELSTL LQEIRNNSNSSDIELEEKVMLTECEINVISNIDTQIVEERIEEAKNLTSDSINYIKDEFKLIESISDALCDLKQQNELED SHFISFEDISETDEGFSIRFINKETGESIFVETEKTIFSEYANHITEEISKIKGTIFDTVNGKLVKKVNLDTTHEVNTLN AAFFIQSLIEYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVSTALDETIDLLPTLSEGLPIIATIIDGVS LGAAIKELSETSDPLLRQEIEAKIGIMAVNLTTATTAIITSSLGIASGFSILLVPLAGISAGIPSLVNNELVLRDKATKV VDYFKHVSLVETEGVFTLLDDKIMMPQDDLVISEIDFNNNSIVLGKCEIWRMEGGSGHTVTDDIDHFFSAPSITYREPHL SIYDVLEVQKEELDLSKDLMVLPNAPNRVFAWETGWTPGLRSLENDGTKLLDRIRDNYEGEFYWRYFAFIADALITTLKP RYEDTNIRINLDSNTRSFIVPIITTEYIREKLSYSFYGSGGTYALSLSQYNMGINIELSESDVWIIDVDNVVRDVTIESD KIKKGDLIEGILSTLSIEENKIILNSHEINFSGEVNGSNGFVSLTFSILEGINAIIEVDLLSKSYKLLISGELKILMLNS NHIQQKIDYIGFNSELQKNIPYSFVDSEGKENGFINGSTKEGLFVSELPDVVLISKVYMDDSKPSFGYYSNNLKDVKVIT KDNVNILTGYYLKDDIKISLSLTLQDEKTIKLNSVHLDESGVAEILKFMNRKGNTNTSDSLMSFLESMNIKSIFVNFLQS NIKFILDANFIISGTTSIGQFEFICDENDNIQPYFIKFNTLETNYTLYVGNRQNMIVEPNYDLDDSGDISSTVINFSQKY LYGIDSCVNKVVISPNIYTDEINITPVYETNNTYPEVIVLDANYINEKINVNINDLSIRYVWSNDGNDFILMSTSEENKV SQVKIRFVNVFKDKTLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYDLGLVSLYNEKFYINNFGMMVSGLIYIND SLYYFKPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENLEG EAIDFTGKLIIDENIYYFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHYFD DSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAVVGWK DLEDGSKYYFDEDTAEAYIGLSLINDGQYYFNDDGIMQVGFVTINDKVFYFSDSGIIESGVQNIDDNYFYIDDNGIVQIG VFDTSDGYKYFAPANTVNDNIYGQAVEYSGLVRVGEDVYYFGETYTIETGWIYDMENESDKYYFNPETKKACKGINLIDD IKYYFDEKGIMRTGLISFENNNYYFNENGEMQFGYINIEDKMFYFGEDGVMQIGVFNTPDGFKYFAHQNTLDENFEGESI NYTGWLDLDEKRYYFTDEYIAATGSVIIDGEEYYFDPDTAQLVISEHHHHHH P18177 3.4.22.- TAUROCHENODEOXYCHOLIC ACID 0.000499704 3 TUD singleParticle particle 2 8.0 50.0 NaCl sodium chloride 20.0 Tris
500 micromolar of TCDCA was added before freezing.
 Homemade COPPER 400 GOLD HOLEY GLOW DISCHARGE AIR 4.0 ETHANE 80 277 LEICA EM GP
30s preblot incubation on grid. 2-3s blot time..
Purified TcdB was mixed with 500 micromolar of TCDCA (4% DMSO final concentration) and incubated on ice until plunge freezing.
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 2.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 40.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 FOURIER SPACE 3.28 FSC 0.143 CUT-OFF 351161 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_70486.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 395.52 395.52 395.52 90.0 90.0 90.0 X Y Z -0.30634803 0.6468575 -0.00008384371 0.012200308 1.03 1.03 1.03 0.107 AUTHOR cryoEM map of Toxin B (TcdB) from Clostridioides difficile complexed with the natural bile acid TCDCA. P18177 AlphaFold in silico model OTHER
Predicted models were docked into the map using ChimeraX. The model was then manually built with ISOLDE and Coot and refined with phenix.real_space_refine.
REAL emd_70486_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 395.52 395.52 395.52 90.0 90.0 90.0 X Y Z -0.4132776 0.7772901 0.00010902043 0.025438126 1.03 1.03 1.03 AUTHOR Half map B of Toxin B (TcdB) from Clostridioides difficile complexed with the natural bile acid TCDCA. emd_70486_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 395.52 395.52 395.52 90.0 90.0 90.0 X Y Z -0.35843715 0.804951 0.00010619558 0.025422262 1.03 1.03 1.03 AUTHOR Half map A of Toxin B (TcdB) from Clostridioides difficile complexed with the natural bile acid TCDCA.