7V1N: Clade 2 C. difficile TcdB

Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI. Determined by electron microscopy at 3.2 Å resolution. Released 23 Feb 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Clostridioides difficile, Homo sapiens
Chains: 2
Atoms: 19,156
Mol. weight: 299.14 kDa
Released: 23 Feb 2022

Explore 7V1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V1N contains 60 α-helices and 164 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: 59 helices, 161 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-12	7
α-helix	27-30	4
α-helix	49-52	4
α-helix	54-62	9
β-strand	92-93	2	1
α-helix	94-95	2
β-strand	97-101	5	2
α-helix	109-121	13
β-strand	126-131	6	2
α-helix	138-153	16
α-helix	155-158	4
α-helix	168-170	3
α-helix	176-196	21
α-helix	202-214	13
α-helix	220-226	7
β-strand	237-239	3	2
α-helix	257-260	4
α-helix	265-279	15
β-strand	282-285	4	2
β-strand	290	1	3
α-helix	310-324	15
α-helix	341-344	4
α-helix	346-352	7
α-helix	357-360	4
α-helix	362-363	2
β-strand	368-369	2	1
β-strand	375-378	4	2
β-strand	383-390	8	2
α-helix	396-420	25
α-helix	425-437	13
α-helix	445-448	4
α-helix	454-456	3
α-helix	466-469	4
α-helix	472-483	12
β-strand	503	1	2
β-strand	510	1	3
α-helix	515-518	4
α-helix	525-537	13
α-helix	556-559	4
β-strand	583-584	2	4
α-helix	589-600	12
β-strand	609-610	2	4
β-strand	646-647	2	5
β-strand	651-652	2	4
β-strand	655	1	6
β-strand	664	1	6
α-helix	669-681	13
α-helix	683-685	3
β-strand	691-693	3	5
β-strand	696-697	2	7
α-helix	712-720	9
α-helix	725-727	3
β-strand	736-737	2	5
β-strand	738	1	8
β-strand	740-741	2	7
β-strand	745-747	3	9
β-strand	753-756	4	9
β-strand	762-763	2	9
α-helix	766-774	9
β-strand	778-781	4	8
β-strand	788-791	4	8
α-helix	795-809	15
α-helix	818-838	21
α-helix	851-862	12
α-helix	871-873	3
β-strand	883	1	10
β-strand	897	1	11
β-strand	902	1	10
β-strand	914	1	11
α-helix	918-935	18
α-helix	983-990	8
α-helix	1093-1096	4
β-strand	1107	1	12
β-strand	1112	1	12
β-strand	1115	1	13
α-helix	1118-1133	16
β-strand	1138	1	14
β-strand	1146	1	14
β-strand	1155-1157	3	15
β-strand	1162-1163	2	15
β-strand	1168-1170	3	13
α-helix	1171	1
β-strand	1172-1173	2	16
β-strand	1182	1	17
β-strand	1185	1	17
β-strand	1186	1	18
β-strand	1193-1194	2	16
β-strand	1228	1	19
β-strand	1229-1237	9	13
α-helix	1247-1258	12
β-strand	1267	1	18
β-strand	1268	1	20
β-strand	1273	1	20
β-strand	1274-1281	8	13
β-strand	1284	1	19
β-strand	1289-1291	3	15
α-helix	1307-1311	5
β-strand	1314-1318	5	15
β-strand	1323-1327	5	21
β-strand	1334-1338	5	15
β-strand	1344-1348	5	21
α-helix	1350-1353	4
β-strand	1356-1359	4	22
β-strand	1362-1365	4	22
α-helix	1368-1369	2
β-strand	1376-1378	3	23
β-strand	1382	1	15
β-strand	1383-1385	3	23
β-strand	1388	1	23
β-strand	1391-1393	3	15
β-strand	1403-1408	6	21
β-strand	1413-1420	8	21
β-strand	1425-1427	3	21
β-strand	1430-1432	3	21
α-helix	1434-1450	17
β-strand	1455	1	24
β-strand	1457	1	24
β-strand	1460-1464	5	21
β-strand	1473-1477	5	21
β-strand	1483	1	25
β-strand	1486-1489	4	26
β-strand	1492-1496	5	26
β-strand	1498	1	25
α-helix	1505-1507	3
β-strand	1508-1511	4	26
β-strand	1542-1545	4	27
β-strand	1550-1557	8	27
α-helix	1562-1571	10
α-helix	1581-1588	8
β-strand	1596	1	26
β-strand	1602	1	26
β-strand	1604-1606	3	27
β-strand	1612-1614	3	27
β-strand	1616	1	27
β-strand	1621-1625	5	27
β-strand	1633-1638	6	27
β-strand	1644-1647	4	28
β-strand	1655-1660	6	28
β-strand	1678	1	29
α-helix	1679-1681	3
β-strand	1691-1694	4	28
β-strand	1702-1705	4	30
β-strand	1706	1	29
β-strand	1717-1720	4	28
β-strand	1730-1734	5	30
β-strand	1741-1746	6	28
β-strand	1749-1754	6	28
β-strand	1765-1769	5	28
β-strand	1781-1784	4	30
β-strand	1791-1792	2	30
α-helix	1793-1798	6
β-strand	1802	1	28
β-strand	1815-1819	5	31
β-strand	1822-1826	5	31
β-strand	1832	1	31
β-strand	1835-1837	3	32
α-helix	1839-1841	3
β-strand	1844-1846	3	32
β-strand	1853	1	32
β-strand	1857-1860	4	33
β-strand	1863-1866	4	33
α-helix	1869-1871	3
β-strand	1878-1882	5	34
β-strand	1885-1889	5	34
β-strand	1895	1	34
β-strand	1898-1900	3	35
β-strand	1907-1910	4	35
β-strand	1922-1923	2	35
β-strand	1928-1932	5	36
β-strand	1935-1939	5	36
β-strand	1951-1952	2	37
β-strand	1955-1956	2	37
β-strand	1969-1972	4	38
β-strand	1977-1980	4	38
β-strand	1986	1	38
β-strand	1992	1	39
β-strand	1997	1	39
β-strand	2011-2013	3	40
β-strand	2016-2018	3	40
β-strand	2030-2032	3	41
β-strand	2037-2039	3	41
β-strand	2040-2041	2	42
β-strand	2053-2054	2	42
β-strand	2059-2063	5	43
β-strand	2066-2070	5	43
β-strand	2076	1	43
β-strand	2081-2083	3	44
β-strand	2086-2089	4	44
β-strand	2145	1	45
β-strand	2148	1	45
β-strand	2152-2153	2	46
β-strand	2157-2158	2	46
β-strand	2171-2172	2	47
β-strand	2186-2187	2	47
β-strand	2191	1	48
β-strand	2202	1	48
β-strand	2208	1	48
β-strand	2235-2239	5	49
β-strand	2242-2246	5	49
β-strand	2252	1	49
β-strand	2257-2258	2	50
β-strand	2263-2264	2	50
β-strand	2266	1	51
α-helix	2271	1
β-strand	2272	1	51
α-helix	2273	1
β-strand	2275	1	52
β-strand	2286	1	52
β-strand	2292	1	52
β-strand	2295-2299	5	53
β-strand	2302-2307	6	53
α-helix	2308	1
β-strand	2319-2320	2	53
β-strand	2327-2328	2	54
β-strand	2333-2334	2	54
β-strand	2346-2349	4	55
β-strand	2352-2355	4	55
β-strand	2356	1	56
β-strand	2363	1	56

Chain K: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	138-144	7	57
β-strand	149-155	7	57
β-strand	165	1	57
α-helix	169-175	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toxin B	A	protein	2375	Clostridioides difficile	Q9EXR0 (AlphaFold model)
Isoform Beta of Tissue factor pathway inhibitor	K	protein	251	Homo sapiens	P10646 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7V1N_1 Toxin B (chains A)
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 (K), FASTA

>7V1N_2 Isoform Beta of Tissue factor pathway inhibitor (chains K)
MIYTMKKVHALWASVCLLLNLAPAPLNADSEEDEEHTIITDTELPPLKLMHSFCAFKADD
GPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRDNANRIIKTTLQQE
KPDFCFLEEDPGICRGYITRYFYNNQTKQCERFKYGGCLGNMNNFETLEECKNICEDGPN
GFQVDNYGTQLNAVNNSLTPQSTKVPSLFVTKEGTNDGWKNAAHIYQVFLNAFCIHASMF
FLGLDSISCLC

Primary citation

TFPI is a colonic crypt receptor for TcdB from hypervirulent clade 2 C. difficile. Luo, J., Yang, Q., Zhang, X. et al. Cell (2022) 185:980-994.e15. DOI 10.1016/j.cell.2022.02.010 · 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
8Y9C 3.0 Å, De novo design mini-binder in complex with TcdB4

Browse structure collections

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