CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B (TcdB)

2026-01-07 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.year _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.year _em_admin.last_update RCSB RCSB 2025-02-21 2025-11-12 2025-11-12 2026-01-07 Howard Hughes Medical Institute (HHMI) United States Department of Energy (DOE, United States) DE-SC0018940 MOD03 United States National Institutes of Health/National Eye Institute (NIH/NEI) T32EY032448 United States National Institutes of Health/National Cancer Institute (NIH/NCI) R01CA260415 United States Bill & Melinda Gates Foundation INV-010680 United States European Molecular Biology Organization (EMBO) ALTF 292-2022 European Union Defense Threat Reduction Agency (DTRA) HDTRA1-21-1-0007 United States National Science Foundation (NSF, United States) NERSC award BER-ERCAP0022018 United States Cancer Research UK CGCATF-2021/100002 United Kingdom National Institutes of Health/National Cancer Institute (NIH/NCI) CA278687-01 United States Defense Threat Reduction Agency (DTRA) HDTRA1-21-1-0038 United States CryoEM Structure of De Novo Antibody Fragment scFv 6 with C. difficile Toxin B (TcdB) Weidle C Borst AJ TcdB, De Novo, scFv 6, De Novo Antibody, DE NOVO PROTEIN Bennett NR Watson JL Ragotte RJ Borst AJ See DL Weidle C Biswas R Yu Y Shrock EL Ault R Leung PJY Huang B Goreshnik I Tam J Carr KD Singer B Criswell C Wicky BIM Vafeados D Garcia Sanchez M Kim HM Vazquez Torres S Chan S Sun SM Spear TT Sun Y O'Reilly K Maris JM Sgourakis NG Melnyk RA Liu CC Baker D Atomically accurate de novo design of antibodies with RFdiffusion. Nature UK 649 183 193 2026 41193805 doi:10.1038/s41586-025-09721-5 1476-4687 0006 NATUAS 9nfu FULLOVERLAP EMDB EMD-49373 associated EM volume

Toxin B in complex with scFv 6 Toxin B in complex with scFv 6 0 1

Toxin B was expressed and purified. scFv 6 was expressed and purified. scFv 6 was mixed with Toxin B at a 3:1 molar ratio.

synthetic construct 0.27117119 Toxin B Clostridioides difficile 0.24122993799999998 1 Priestia megaterium NBRC 15308 = ATCC 14581 LEVO MYMSLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKALKKFKEY LVTEVLELKNNNLTPVEKNLHFVAIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAINDTLESFR ENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGN DVRNFEEFKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLNVNMLPGIQPDLFESIEKPSSVTVDFWEMTKLE AIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNL IVKQIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAY QDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSAGEDDNLDFSQNIVVD KEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPS IISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLK VKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNLPELS TLLQEIRNNSNSSDIELEEKVMLTECEINVISNIDTQIVEERIEEAKNLTSDSINYIKDEFKLIESISDALCDLKQQNEL EDSHFISFEDISETDEGFSIRFINKETGESIFVETEKTIFSEYANHITEEISKIKGTIFDTVNGKLVKKVNLDTTHEVNT LNAAFFIQSLIEYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVSTALDETIDLLPTLSEGLPIIATIIDG VSLGAAIKELSETSDPLLRQEIEAKIGIMAVNLTTATTAIITSSLGIASGFSILLVPLAGISAGIPSLVNNELVLRDKAT KVVDYFKHVSLVETEGVFTLLDDKIMMPQDDLVISEIDFNNNSIVLGKCEIWRMEGGSGHTVTDDIDHFFSAPSITYREP HLSIYDVLEVQKEELDLSKDLMVLPNAPNRVFAWETGWTPGLRSLENDGTKLLDRIRDNYEGEFYWRYFAFIADALITTL KPRYEDTNIRINLDSNTRSFIVPIITTEYIREKLSYSFYGSGGTYALSLSQYNMGINIELSESDVWIIDVDNVVRDVTIE SDKIKKGDLIEGILSTLSIEENKIILNSHEINFSGEVNGSNGFVSLTFSILEGINAIIEVDLLSKSYKLLISGELKILML NSNHIQQKIDYIGFNSELQKNIPYSFVDSEGKENGFINGSTKEGLFVSELPDVVLISKVYMDDSKPSFGYYSNNLKDVKV ITKDNVNILTGYYLKDDIKISLSLTLQDEKTIKLNSVHLDESGVAEILKFMNRKGNTNTSDSLMSFLESMNIKSIFVNFL QSNIKFILDANFIISGTTSIGQFEFICDENDNIQPYFIKFNTLETNYTLYVGNRQNMIVEPNYDLDDSGDISSTVINFSQ KYLYGIDSCVNKVVISPNIYTDEINITPVYETNNTYPEVIVLDANYINEKINVNINDLSIRYVWSNDGNDFILMSTSEEN KVSQVKIRFVNVFKDKTLANKLSFNFSDKQDVPVSEIILSFTPSYYEDGLIGYDLGLVSLYNEKFYINNFGMMVSGLIYI NDSLYYFKPPVNNLITGFVTVGDDKYYFNPINGGAASIGETIIDDKNYYFNQSGVLQTGVFSTEDGFKYFAPANTLDENL EGEAIDFTGKLIIDENIYYFDDNYRGAVEWKELDGEMHYFSPETGKAFKGLNQIGDYKYYFNSDGVMQKGFVSINDNKHY FDDSGVMKVGYTEIDGKHFYFAENGEMQIGVFNTEDGFKYFAHHNEDLGNEEGEEISYSGILNFNNKIYYFDDSFTAVVG WKDLEDGSKYYFDEDTAEAYIGGYRPHAGLRGSHHHHHH P18177 3.4.22.- scFv 6 Heavy Chain, scFv 6 Light Chain synthetic construct 0.030211605

Heavy Chain with Linker to Light Chain

1 Cricetulus griseus LEVO MGWSCIILFLVATATGVHSEVQLVESGGGLVQPGGSLRLSCAASGFSIKNTYIHWVRQAPGKGLEWVARIWPANGKTRYA DSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRQLDPYNLYGNDVWGQGTLVTVSSPNSASHSGSAPQTSSAPGSD IQMTQSPSSLSASVGDRVTITCKTSSSYVNWYQQKPGKAPKLLIYRNSFRAPGVPSRFSGSRSGTDFTLTISSLQPEDFA TYYCSTMNNDGNLVFGQGTKVEIKENLYFQGSHHHHHH singleParticle particle 0.81 7.5 150.0 NaCl sodium chloride 40.0 Tris/HCl tris(hydroxymethyl)aminomethane/Hydrochloric Acid

150 mM NaCl, 40 mM Tris/ HCl pH 7.5

C-flat-2/2 COPPER 300 CARBON HOLEY 40.0 GLOW DISCHARGE 25 AIR 39.0

15 mA current

ETHANE 100 295.15 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.8 1.8 45000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum GATAN K3 (6k x 4k) 1 10897 5.0 44.0 1 3357543

Patch CTF

PHASE FLIPPING AND AMPLITUDE CORRECTION

3D Ab Initio

1 C1 FOURIER SPACE 3.6 FSC 0.143 CUT-OFF

Non Uniform Refinement

19969 MAXIMUM LIKELIHOOD

Non Uniform Refinement

MAXIMUM LIKELIHOOD

Non Uniform Refinement

2 17141.0

3D Classification

emd_49373.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 407.1 407.1 407.1 90.0 90.0 90.0 X Y Z -0.12292408 0.24755934 -0.00001685791 0.00441912 0.885 0.885 0.885 0.0339 AUTHOR ::::EMDATABANK.org::::EMD-49373:::: 6OQ5 PDB experimental model

TcdB

Other in silico model

De Novo Design

FLEXIBLE FIT

TcdB was built using the published 3.87 Angstrom crystal structure as a starting model (PDB: 6OQ5). The three bound VHH domains in the crystal structure were removed in PyMOL, and the structure was docked into density using Chimera. The initial model was refined in Coot before alignment with the design model in PyMOL, the scFv docked well in density. The entire model was refined with iterative rounds in Coot, Interactive Structure Optimization by Local Direct Exploration (ISOLDE) were performed at a simulated 25 Kelvin, and Phenix real-space refinement. The final model quality was analyzed using Molprobity.

REAL emd_49373_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 407.1 407.1 407.1 90.0 90.0 90.0 X Y Z -0.046395656 0.12991713 -0.00001685791 0.0029558528 0.885 0.885 0.885 AUTHOR ::::EMDATABANK.org::::EMD-49373:::: emd_49373_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 407.1 407.1 407.1 90.0 90.0 90.0 X Y Z -0.26718003 0.31520408 0.000022630742 0.025646929 0.885 0.885 0.885 AUTHOR ::::EMDATABANK.org::::EMD-49373:::: emd_49373_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 460 460 460 0 0 0 460 460 460 407.1 407.1 407.1 90.0 90.0 90.0 X Y Z -0.2303631 0.29283193 0.000022683325 0.025481805 0.885 0.885 0.885 AUTHOR ::::EMDATABANK.org::::EMD-49373::::