8Y9C: De novo design mini-binder

De novo design mini-binder in complex with TcdB4. Determined by electron microscopy at 3.0 Å resolution. Released 28 Aug 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Clostridioides difficile, synthetic construct
Chains: 2
Atoms: 13,400
Mol. weight: 277.96 kDa
Ligands: ZN
Released: 28 Aug 2024

Explore 8Y9C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y9C contains 69 α-helices and 92 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	3-17	15
β-strand	22-25	4	22
β-strand	31-35	5	22
α-helix	40-56	17
β-strand	60-62	3	22

Chain B: 67 helices, 89 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	22-35	14
α-helix	42-62	21
β-strand	66	1	1
α-helix	69-89	21
β-strand	92-93	2	2
α-helix	94-95	2
β-strand	98-101	4	3
α-helix	106-108	3
α-helix	109-121	13
β-strand	127-131	5	3
α-helix	138-157	20
α-helix	158-160	3
α-helix	168-196	29
α-helix	202-214	13
α-helix	218-233	16
β-strand	237-239	3	3
α-helix	244-247	4
α-helix	252-256	5
α-helix	257-261	5
α-helix	265-279	15
β-strand	282-285	4	3
β-strand	290-291	2	4
α-helix	292	1
β-strand	293	1	5
α-helix	294	1
α-helix	302-304	3
α-helix	310-324	15
α-helix	334-337	4
α-helix	341-352	12
β-strand	361	1	5
β-strand	368-369	2	2
β-strand	375-379	5	3
β-strand	382-390	9	3
α-helix	395-419	25
α-helix	425-439	15
α-helix	445-448	4
α-helix	454-456	3
α-helix	465-470	6
α-helix	472-484	13
α-helix	496-499	4
α-helix	500-502	3
β-strand	503	1	3
α-helix	506-508	3
β-strand	509-510	2	4
α-helix	514-519	6
α-helix	525-539	15
α-helix	556-558	3
α-helix	560-568	9
β-strand	579-584	6	6
α-helix	589-601	13
β-strand	606-610	5	6
β-strand	618-623	6	6
β-strand	628-633	6	6
α-helix	639-641	3
β-strand	646-654	9	6
β-strand	655	1	7
β-strand	664	1	7
β-strand	667	1	7
α-helix	669-683	15
β-strand	691-699	9	6
α-helix	708-710	3
α-helix	712-727	16
α-helix	733-735	3
β-strand	736-741	6	6
β-strand	745-747	3	8
β-strand	753-756	4	8
β-strand	762-763	2	8
α-helix	766-775	10
β-strand	778-782	5	6
β-strand	787-790	4	6
α-helix	795-809	15
α-helix	816-838	23
α-helix	851-876	26
β-strand	883-884	2	9
β-strand	891-892	2	9
β-strand	897-903	7	9
β-strand	909-914	6	9
α-helix	918-934	17
β-strand	937-941	5	10
β-strand	944-947	4	10
α-helix	948	1
α-helix	959-970	12
α-helix	982-993	12
α-helix	1005-1017	13
α-helix	1055-1068	14
α-helix	1071-1076	6
β-strand	1344-1346	3	11
α-helix	1349-1352	4
β-strand	1378	1	12
β-strand	1383	1	12
β-strand	1404-1408	5	11
β-strand	1413-1420	8	11
β-strand	1425-1432	8	11
α-helix	1434-1439	6
α-helix	1441-1451	11
β-strand	1460-1466	7	11
β-strand	1471-1477	7	11
β-strand	1482-1488	7	11
β-strand	1493-1499	7	11
β-strand	1507-1511	5	11
β-strand	1515-1521	7	13
β-strand	1526-1534	9	13
β-strand	1537-1545	9	13
β-strand	1550-1558	9	13
α-helix	1560-1573	14
α-helix	1581-1588	8
β-strand	1595-1596	2	11
β-strand	1602	1	11
β-strand	1604-1616	13	13
β-strand	1620-1626	7	13
β-strand	1632-1641	10	13
β-strand	1644-1649	6	13
α-helix	1650-1652	3
β-strand	1655-1660	6	13
β-strand	1664	1	14
β-strand	1669	1	1
β-strand	1670	1	14
β-strand	1674-1678	5	15
α-helix	1679-1682	4
α-helix	1686-1688	3
β-strand	1691-1694	4	13
β-strand	1702-1706	5	15
α-helix	1716	1
β-strand	1717-1720	4	13
β-strand	1730-1734	5	15
α-helix	1738-1740	3
β-strand	1741-1746	6	13
β-strand	1749-1754	6	13
β-strand	1765-1768	4	13
α-helix	1778-1780	3
β-strand	1781-1784	4	15
β-strand	1791-1792	2	15
α-helix	1793-1799	7
α-helix	1801	1
β-strand	1802	1	13
β-strand	1815-1819	5	16
β-strand	1822-1826	5	16
β-strand	1832	1	16
β-strand	1835-1839	5	17
β-strand	1842-1846	5	17
β-strand	1853	1	17
β-strand	1856-1860	5	18
β-strand	1863-1868	6	18
β-strand	1874-1875	2	18
α-helix	1876	1
β-strand	1878-1882	5	19
β-strand	1885-1889	5	19
β-strand	1895	1	19
β-strand	1898-1902	5	20
β-strand	1905-1909	5	20
α-helix	1918-1919	2
β-strand	1923	1	20
β-strand	1928-1932	5	21
β-strand	1935-1939	5	21
β-strand	1945	1	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toxin B	B	protein	2375	Clostridioides difficile	Q9EXR0 (AlphaFold model)
De novo design Minibinder	A	protein	65	synthetic construct

Sequence of entity 1 (B), FASTA

>8Y9C_1 Toxin B (chains B)
MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDTYI
DTYKKSGRNKALKKFKEYLVTEILELKNSNLTPVEKNLHFIWIGGQINDTAINYINQWKD
VNSDYNVNVFYDSNAFLINTLKKTIIESASNDTLESFRENLNDPEFNHTAFFRKRMQIIY
DKQQNFINYYKAQKEENPDLIIDDIVKTYLSNEYSKDIDELNAYIEESLNKVTENSGNDV
RNFEEFKTGEVFNLYEQELVERWNLAGASDILRVAILKNIGGVYLDVDMLPGIHPDLFKD
INKPDSVKTAVDWEEMQLEAIMKYKEYIPEYTSKHFDTLDEEVQSSFESVLASKSDKSEI
FLPLGDIEVSPLEVKVAFAKGSIINQALISAKDSYCSDLLIKQIQNRYKILNDTLGPIIS
QGNDFNTTMNNFGESLGAIANEENISFIAKIGSYLRVGFYPEANTTITLSGPTIYAGAYK
DLLTFKEMSIDTSILSSELRNFEFPKVNISQATEQEKNSLWQFNEERAKIQFEEYKKNYF
EGALGEDDNLDFSQNTVTDKEYLLEKISSSTKSSERGYVHYIVQLQGDKISYEAACNLFA
KNPYDSILFQKNIEDSEVAYYYNPTDSEIQEIDKYRIPDRISDRPKIKLTLIGHGKAEFN
TDIFAGLDVDSLSSEIETIIDLAKADISPKSIEINLLGCNMFSYSVNVEETYPGKLLLRV
KDKVSELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYIS
FNPKENKIIVKSKNLPELSTLLQEIRNNSNSSDIELEEKVMLAECEINVISNIETQVVEE
RIEEAKSLTSDSINYIKNEFKLIESISDALYDLKQQNELEESHFISFEDISKTDEGFSIR
FIDKETGESIFVETEKAIFSEYANHITEEISKLKDTIFDTVNGKLVKKVTLDATHEVNTL
NAAFFIQSLIGYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVSTALDETI
DLLPTLSEGLPVIATIIDGVSLGASIKELSETSDPLLRQEIEAKIGIMAVNLTAATTAII
TSSLGIASGFSILLVPLAGISAGIPSLVNNELILRAEAKNVVDYFGHISLAESEGAFTLL
DDKIMMPQDDLVISEIDFNNNSITLGKCEIWRMEGGSGHTVTDDIDHFFSAPSTTYREPY
LSIYDVLDVKKEELDLSKDLMVLPNAPDRIFGWERGWTPGLRSLENDGTKLLDRIRDHYE
GQFYWRFFAFIADSVITKLKPRYEDTNIRISLDSNTRSFIVPVITTEYIREKLSYSFYGS
GGTYALSLSQYNMNINIELNENDTWVIDVDNVVRDVTIESDKIKKGDLIENILSKLSIED
NKIILDNHEINFSGTLNGGNGFVSLTFSILEGINAVIEVDLLSKSYKVLISGELKTLMAN
SNSVQQKIDYIGLNSELQKNIPYSFMDDEGKENGFINCFTKEGLFVSELSDVVLIIKVYM
DNSKPPFGYYSNDLKDVKVITKDDVIILTGYYLKDDIKISLSFTIQDKNTIKLNGVYLDE
NGVAEILKFMNKKGSTNTSDSLMSFLESMNIKSIFIKSLKSNAKLILDTNFIISGTTSIG
QFEFICDKDNNIQPYFIKFNTLETKYTLYVGNRQNMIVEPNYNLDDSGDISSTVINFSQK
YLYGIDSCVNKVIISPNIYTDEINITPVHEANNTYPEVIVLDTNYISEKINININDLSIR
YVWSNDGSDFILMSTDEENKVSQVKIRFTNVFKGNTISDKISFNFSDKQDISINKIISTF
TPSYYVEGLLNYDLGLISLYNEKFYINNLGMMVSGLVYINDSLYYFKPPIKNLITGFTTI
GDDKYYFNPDNGGAASVGETIIDGKNYYFSQNGVLQTGVFSTEDGFKYFAPADTLDENLE
GEAIDFTGKLIIDENVYYFGDNYRAAIEWQTLDDEVYYFSTDTGRAFKGLNQIGDDKFYF
NSDGIMQKGFVNINDKTFYFDDSGVMKSGYTEIDGKYFYFAENGEMQIGVFNTADGFKYF
AHHDEDLGNEEGEALSYSGILNFNNKIYYFDDSFTAVVGWKDLEDGSKYYFDENTAEASI
GISIINDGKYYFNDSGIMQIGFVTINNEVFYFSDSGIVESGMQNIDDNYFYISENGLVQI
GVFDTSDGYKYFAPANTVNDNIYGQAVEYSGLVRVNEDVYSFGESYTIETGWIYDSENES
DKYYFDPETKKAYKGINVIDDIKYYFDENGIMRTGLITFEDNHYYFNEDGEMQYGYLNIE
DKMFYFSEDGIMQIGVFNTPDGFKYFAHQNTLDENFEGESINYTGWLDLDEKRYYFTDEY
IAATGSVIIDGEEYYFDPDTAQLVISEHHHHHHHH

Sequence of entity 2 (A), FASTA

>8Y9C_2 De novo design Minibinder (chains A)
NEEEKFKFFVWFLAIRAGVPEVEVRNDNGKFQVTVKGDTDAARLLTKEVKEVATFLGVDV
DLQIR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

De novo design of mini-protein binders broadly neutralizing Clostridioides difficile toxin B variants. Lv, X., Zhang, Y., Sun, K. et al. Nat Commun (2024) 15:8521-8521. DOI 10.1038/s41467-024-52582-1 · PubMed

Other PDB entries of the same protein (UniProt Q9EXR0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7S0Z 2.34 Å, Structures of TcdB in complex with R-Ras
6OQ7 2.39 Å, Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3
7V1N 3.2 Å, Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI

Browse structure collections

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