2025-10-08 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2024-12-09 2025-09-17 2025-09-17 2025-10-08 Canadian Institutes of Health Research (CIHR) 452580 Canada De novo designed minibinder complexed with Clostridioides difficile Toxin B Miletic S Li Z Ragotte RJ Melnyk R TcdB, minibinder, de novo, inhibitor, TOXIN Ragotte RJ Liang H Tam J Miletic S Berman JM Palou R Weidle C Li Z Glogl M Beilhartz GL Carr KD Borst AJ Coventry B Wang X Rubinstein JL Tyers M Schramek D Melnyk RA Baker D De novo design of potent inhibitors of clostridial family toxins. Proc.Natl.Acad.Sci.USA US 122 e2509329122 e2509329122 2025 40982695 doi:10.1073/pnas.2509329122 1091-6490 0040 PNASA6 9mf4 FULLOVERLAP EMDB EMD-48223 associated EM volume
De novo designed minibinder complexed with Clostridioides difficile Toxin B
 De novo designed minibinder complexed with Clostridioides difficile Toxin B De novo designed minibinder complexed with Clostridioides difficile Toxin B 0 1 2 Clostridioides difficile VPI 10463 0.278 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.- De novo designed cspg67 minibinder synthetic construct 0.006640785
De novo designed mini protein inhibitor (minibinder) targeting CSPG4 receptor binding site on TcdB
1 Escherichia coli BL21 LEVO AEELAKKLEEMAEVFKEKGDEEGAKECLKAAKIVRRSKNEEFGKWCIKKAEERLKKL singleParticle particle 2 8.0 50.0 NaCl sodium chloride 20.0 tris 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 CSPG4 minibinder #67 at a 1:1 molar ratio 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) 42.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 FOURIER SPACE 3.02 FSC 0.143 CUT-OFF cryoSPARC 4 179414 MAXIMUM LIKELIHOOD cryoSPARC 4 MAXIMUM LIKELIHOOD cryoSPARC 4 cryoSPARC 4 emd_48223.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 329.59998 329.59998 329.59998 90.0 90.0 90.0 X Y Z -0.087857015 0.24417086 0.00005466425 0.0043926286 1.03 1.03 1.03 0.0432 AUTHOR Map of TcdB bound to CSPG4 site minibinder P18177 AlphaFold in silico model OTHER
Predicted models were docked into the map using ChimeraX. The model was then manually with ISOLDE and refined with phenix.real_space_refine.
113.0 emd_48223_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 329.59998 329.59998 329.59998 90.0 90.0 90.0 X Y Z -0.09782809 0.25390637 0.00013018462 0.0066601653 1.03 1.03 1.03 AUTHOR Half map A of TcdB bound to CSPG4 site minibinder emd_48223_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 329.59998 329.59998 329.59998 90.0 90.0 90.0 X Y Z -0.09824555 0.24734367 0.00013119052 0.0066152336 1.03 1.03 1.03 AUTHOR Half map B of TcdB bound to CSPG4 site minibinder