6L7E: Toxin Complex TcdA1-TcdB1-TccC2

Name: PDB 6L7E: Toxin Complex TcdA1-TcdB1-TccC2
Published: 2020-11-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Toxin Complex TcdA1-TcdB1-TccC2. Determined by electron microscopy at 3.2 Å resolution. Released 4 Nov 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Photorhabdus luminescens
Chains: 5
Atoms: 97,400
Mol. weight: 1416.15 kDa
Released: 4 Nov 2020

Explore 6L7E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L7E contains 565 α-helices and 565 β-strands across 5 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.

Chains A, B, C, D and E: 113 helices, 113 β-strands

Element	Residues	Length	Sheet
α-helix	43-69	27
α-helix	72-76	5
α-helix	78-80	3
α-helix	88-95	8
β-strand	104	1	1
β-strand	111	1	2
α-helix	115-126	12
β-strand	130	1	3
α-helix	138-141	4
β-strand	149	1	4
α-helix	152-156	5
β-strand	159-160	2	5
α-helix	161-176	16
α-helix	182-191	10
α-helix	202-214	13
α-helix	220-223	4
α-helix	225-228	4
α-helix	233-240	8
α-helix	245-251	7
α-helix	260-268	9
α-helix	273-276	4
α-helix	279-285	7
α-helix	290-293	4
β-strand	299-300	2	6
β-strand	306-307	2	6
β-strand	312-318	7	7
α-helix	319	1
β-strand	325-335	11	7
β-strand	341-347	7	8
β-strand	352-359	8	8
β-strand	367-372	6	7
β-strand	376-382	7	7
α-helix	384-386	3
β-strand	387	1	8
β-strand	391-396	6	8
α-helix	399-402	4
β-strand	406-413	8	7
β-strand	419-432	14	7
α-helix	433-450	18
α-helix	454-464	11
α-helix	472-487	16
α-helix	492-497	6
α-helix	502-504	3
α-helix	514-519	6
β-strand	524	1	9
β-strand	527	1	9
β-strand	536	1	10
α-helix	546-555	10
α-helix	559-569	11
β-strand	578	1	10
α-helix	582-596	15
α-helix	602-612	11
α-helix	624-644	21
α-helix	648-655	8
α-helix	665-677	13
α-helix	688-697	10
α-helix	705-718	14
α-helix	727-736	10
α-helix	744-746	3
α-helix	749-768	20
α-helix	773-781	9
α-helix	783-786	4
α-helix	788-789	2
α-helix	793-795	3
α-helix	798-812	15
α-helix	815-817	3
α-helix	818-826	9
α-helix	832-838	7
α-helix	843-854	12
α-helix	871-884	14
α-helix	891-898	8
α-helix	904-906	3
α-helix	912-923	12
α-helix	928-949	22
α-helix	950-954	5
α-helix	964-971	8
β-strand	982-983	2	5
α-helix	985-1000	16
β-strand	1008	1	3
α-helix	1010-1013	4
α-helix	1016-1019	4
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1055-1063	9
α-helix	1071-1089	19
β-strand	1096-1098	3	11
β-strand	1107-1110	4	11
β-strand	1122-1123	2	12
β-strand	1125-1127	3	11
α-helix	1128-1130	3
β-strand	1131-1132	2	13
β-strand	1135-1136	2	13
α-helix	1143-1144	2
β-strand	1145-1146	2	12
β-strand	1158-1162	5	14
β-strand	1167-1180	14	14
β-strand	1190-1202	13	14
β-strand	1203	1	15
β-strand	1209	1	15
α-helix	1210-1212	3
β-strand	1215-1216	2	14
α-helix	1218-1223	6
α-helix	1231-1232	2
β-strand	1233-1239	7	16
β-strand	1244-1250	7	16
β-strand	1253	1	17
α-helix	1256-1260	5
β-strand	1265-1269	5	16
β-strand	1275-1277	3	16
α-helix	1278-1279	2
α-helix	1280-1288	9
α-helix	1291-1293	3
β-strand	1296	1	17
β-strand	1300-1302	3	18
β-strand	1303	1	11
α-helix	1304-1306	3
β-strand	1310-1311	2	19
β-strand	1316	1	20
β-strand	1321-1323	3	21
β-strand	1324	1	22
α-helix	1326-1328	3
β-strand	1331-1332	2	22
β-strand	1336	1	22
β-strand	1337	1	20
β-strand	1340-1345	6	23
β-strand	1348-1353	6	23
β-strand	1356-1360	5	22
α-helix	1369-1377	9
β-strand	1384-1393	10	24
β-strand	1407-1409	3	24
β-strand	1421-1425	5	24
β-strand	1432-1438	7	24
β-strand	1443-1450	8	24
β-strand	1454-1458	5	24
α-helix	1464-1466	3
β-strand	1471-1474	4	24
β-strand	1480-1490	11	24
β-strand	1499-1503	5	21
β-strand	1508-1512	5	21
β-strand	1517	1	25
α-helix	1520-1523	4
β-strand	1528-1531	4	22
β-strand	1532	1	25
β-strand	1535-1538	4	23
β-strand	1545	1	19
β-strand	1548-1551	4	19
β-strand	1552-1558	7	21
β-strand	1564-1569	6	21
β-strand	1572-1576	5	19
α-helix	1577-1578	2
α-helix	1582-1583	2
β-strand	1584-1588	5	18
β-strand	1594-1598	5	18
β-strand	1601-1604	4	18
α-helix	1609-1612	4
α-helix	1621-1624	4
α-helix	1627-1630	4
β-strand	1633-1635	3	26
β-strand	1640-1647	8	27
α-helix	1648-1650	3
β-strand	1660-1666	7	28
β-strand	1673-1680	8	28
β-strand	1686-1693	8	27
β-strand	1705-1710	6	28
β-strand	1724-1727	4	28
β-strand	1733-1735	3	28
β-strand	1746-1750	5	27
β-strand	1755-1757	3	26
α-helix	1765-1769	5
α-helix	1770-1774	5
α-helix	1775-1785	11
α-helix	1789-1796	8
β-strand	1800	1	29
β-strand	1806	1	30
β-strand	1811	1	30
β-strand	1816	1	29
α-helix	1819-1822	4
α-helix	1837-1843	7
α-helix	1846-1868	23
α-helix	1873-1885	13
α-helix	1887-1890	4
α-helix	1893-1894	2
β-strand	1906	1	4
α-helix	1907-1910	4
α-helix	1913-1927	15
α-helix	1947-1948	2
β-strand	1949	1	2
α-helix	1950	1
β-strand	1951	1	1
α-helix	1954-1971	18
β-strand	1974	1	31
β-strand	1980	1	31
α-helix	1983-1985	3
α-helix	1987-1995	9
α-helix	2000-2002	3
α-helix	2004-2007	4
α-helix	2009-2012	4
β-strand	2017	1	32
α-helix	2019-2104	86
α-helix	2109-2120	12
α-helix	2125-2138	14
β-strand	2144-2146	3	33
β-strand	2148-2150	3	33
α-helix	2156-2243	88
α-helix	2248-2283	36
α-helix	2306-2322	17
β-strand	2329-2336	8	34
α-helix	2337-2341	5
α-helix	2353-2362	10
β-strand	2369-2370	2	35
β-strand	2373-2374	2	35
β-strand	2375-2377	3	36
β-strand	2387-2392	6	36
α-helix	2399-2401	3
β-strand	2410-2418	9	34
β-strand	2421	1	37
β-strand	2431-2435	5	36
β-strand	2449-2450	2	36
β-strand	2456	1	34
β-strand	2468	1	32
α-helix	2469-2470	2
β-strand	2476	1	34
β-strand	2481-2486	6	36
α-helix	2500-2502	3
β-strand	2504	1	37
β-strand	2508-2515	8	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdA1	A, B, C, D, E	protein	2516	Photorhabdus luminescens	Q9RN43

Sequence of entity 1 (A, B, C, D, E), FASTA

>6L7E_1 TcdA1 (chains A, B, C, D, E)
MNESVKEIPDVLKSQCGFNCLTDISHSSFNEFRQQVSEHLSWSETHDLYHDAQQAQKDNR
LYEARILKRANPQLQNAVHLAILAPNAELIGYNNQFSGRASQYVAPGTVSSMFSPAAYLT
ELYREARNLHASDSVYYLDTRRPDLKSMALSQQNMDIELSTLSLSNELLLESIKTESKLE
NYTKVMEMLSTFRPSGATPYHDAYENVREVIQLQDPGLEQLNASPAIAGLMHQASLLGIN
ASISPELFNILTEEITEGNAEELYKKNFGNIEPASLAMPEYLKRYYNLSDEELSQFIGKA
SNFGQQEYSNNQLITPVVNSSDGTVKVYRITREYTTNAYQMDVELFPFGGENYRLDYKFK
NFYNASYLSIKLNDKRELVRTEGAPQVNIEYSANITLNTADISQPFEIGLTRVLPSGSWA
YAAAKFTVEEYNQYSFLLKLNKAIRLSRATELSPTILEGIVRSVNLQLDINTDVLGKVFL
TKYYMQRYAIHAETALILCNAPISQRSYDNQPSQFDRLFNTPLLNGQYFSTGDEEIDLNS
GSTGDWRKTILKRAFNIDDVSLFRLLKITDHDNKDGKIKNNLKNLSNLYIGKLLADIHQL
TIDELDLLLIAVGEGKTNLSAISDKQLATLIRKLNTITSWLHTQKWSVFQLFIMTSTSYN
KTLTPEIKNLLDTVYHGLQGFDKDKADLLHVMAPYIAATLQLSSENVAHSVLLWADKLQP
GDGAMTAEKFWDWLNTKYTPGSSEAVETQEHIVQYCQALAQLEMVYHSTGINENAFRLFV
TKPEMFGAATGAAPAHDALSLIMLTRFADWVNALGEKASSVLAAFEANSLTAEQLADAMN
LDANLLLQASIQAQNHQHLPPVTPENAFSCWTSINTILQWVNVAQQLNVAPQGVSALVGL
DYIQSMKETPTYAQWENAAGVLTAGLNSQQANTLHAFLDESRSAALSTYYIRQVAKAAAA
IKSRDDLYQYLLIDNQVSAAIKTTRIAEAIASIQLYVNRALENVEENANSGVISRQFFID
WDKYNKRYSTWAGVSQLVYYPENYIDPTMRIGQTKMMDALLQSVSQSQLNADTVEDAFMS
YLTSFEQVANLKVISAYHDNINNDQGLTYFIGLSETDAGEYYWRSVDHSKFNDGKFAANA
WSEWHKIDCPINPYKSTIRPVIYKSRLYLLWLEQKEITKQTGNSKDGYQTETDYRYELKL
AHIRYDGTWNTPITFDVNKKISELKLEKNRAPGLYCAGYQGEDTLLVMFYNQQDTLDSYK
NASMQGLYIFADMASKDMTPEQSNVYRDNSYQQFDTNNVRRVNNRYAEDYEIPSSVSSRK
DYGWGDYYLSMVYNGDIPTINYKAASSDLKIYISPKLRIIHNGYEGQKRNQCNLMNKYGK
LGDKFIVYTSLGVNPNNSSNKLMFYPVYQYSGNTSGLNQGRLLFHRDTTYPSKVEAWIPG
AKRSLTNQNAAIGDDYATDSLNKPDDLKQYIFMTDSKGTATDVSGPVEINTAISPAKVQI
IVKAGGKEQTFTADKDVSIQPSPSFDEMNYQFNALEIDGSGLNFINNSASIDVTFTAFAE
DGRKLGYESFSIPVTLKVSTDNALTLHHNENGAQYMQWQSYRTRLNTLFARQLVARATTG
IDTILSMETQNIQEPQLGKGFYATFVIPPYNLSTHGDERWFKLYIKHVVDNNSHIIYSGQ
LTDTNINITLFIPLDDVPLNQDYHAKVYMTFKKSPSDGTWWGPHFVRDDKGIVTINPKSI
LTHFESVNVLNNISSEPMDFSGANSLYFWELFYYTPMLVAQRLLHEQNFDEANRWLKYVW
SPSGYIVHGQIQNYQWNVRPLLEDTSWNSDPLDSVDPDAVAQHDPMHYKVSTFMRTLDLL
IARGDHAYRQLERDTLNEAKMWYMQALHLLGDKPYLPLSTTWSDPRLDRAADITTQNAHD
SAIVALRQNIPTPAPLSLRSANTLTDLFLPQINEVMMNYWQTLAQRVYNLRHNLSIDGQP
LYLPIYATPADPKALLSAAVATSQGGGKLPESFMSLWRFPHMLENARGMVSQLTQFGSTL
QNIIERQDAEALNALLQNQAAELILTNLSIQDKTIEELDAEKTVLEKSKAGAQSRFDSYG
KLYDENINAGENQAMTLRASAAGLTTAVQASRLAGAAADLVPNIFGFAGGGSRWGAIAEA
TGYVMEFSANVMNTEADKISQSETYRRRRQEWEIQRNNAEAELKQIDAQLKSLAVRREAA
VLQKTSLKTQQEQTQSQLAFLQRKFSNQALYNWLRGRLAAIYFQFYDLAVARCLMAEQAY
RWELNDDSARFIKPGAWQGTYAGLLAGETLMLSLAQMEDAHLKRDKRALEVERTVSLAEV
YAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGTDTKTSLQASVSFADLKIRE
DYPASLGKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGLANGCEALAVSHGMNDSGQF
QLDFNDGKFLPFEGIAIDQGTLTLSFPNASMPEKGKQATMLKTLNDIILHIRYTIK

Primary citation

Toxin Complex TcdA1-TcdB1-TccC2. Yan, Z.F., Zhang, N., Yang, G.W. To be published.

Other PDB entries of the same protein (UniProt Q9RN43), best resolution first:

6RW6 2.75 Å, Cryo-EM structure of Photorhabdus luminescens TcdA1
6L7I 2.9 Å, Signal substraction of TcdB1-TccC2 and part of TcdA1
8CPZ 2.9 Å, Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K1179W mutant
8CQ0 3.2 Å, Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567W K2008W mutant
6SUE 3.4 Å, Structure of Photorhabdus luminescens Tc holotoxin pore, Mutation TccC3-D651A
6SUF 3.4 Å, Structure of Photorhabdus luminescens Tc holotoxin pore
5LKH 3.46 Å, Cryo-EM structure of the Tc toxin TcdA1 in its pore state (obtained by flexible fitting)
5LKI 3.46 Å, Cryo-EM structure of the Tc toxin TcdA1 in its pore state
4O9Y 3.5 Å, Crystal Structure of TcdA1
8CQ2 3.6 Å, Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, C16S, C20S, C870S, T1279C…
6H6F 3.72 Å, PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A
6H6E 3.95 Å, PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3)

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