6H6G: TcdB2,TccC3

Name: PDB 6H6G: Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region
Published: 2018-10-03
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region. Determined by X-ray diffraction at 3.0 Å resolution. Released 3 Oct 2018.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Photorhabdus luminescens
Chains: 1
Atoms: 17,194
Mol. weight: 243.77 kDa
Released: 3 Oct 2018

Explore 6H6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6H6G contains 68 α-helices and 167 β-strands across 1 chain. 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: 68 helices, 167 β-strands

Element	Residues	Length	Sheet
β-strand	27-29	3	1
β-strand	38-42	5	1
β-strand	56-60	5	1
β-strand	72-73	2	1
β-strand	78-81	4	2
β-strand	96-97	2	2
α-helix	102	1
β-strand	103	1	2
β-strand	104-106	3	3
β-strand	111-116	6	3
β-strand	119-132	14	3
β-strand	134-135	2	3
β-strand	140-146	7	3
β-strand	154-158	5	3
β-strand	161	1	3
β-strand	164-167	4	3
α-helix	171-173	3
β-strand	174-176	3	2
β-strand	184-188	5	2
β-strand	189-193	5	3
β-strand	199-206	8	3
α-helix	214-219	6
β-strand	227-236	10	3
α-helix	249-252	4
α-helix	253-255	3
β-strand	256-263	8	3
α-helix	281-283	3
β-strand	290-292	3	4
β-strand	299-301	3	4
β-strand	307-312	6	3
α-helix	314-317	4
β-strand	328-338	11	3
β-strand	345-354	10	3
β-strand	360-362	3	3
β-strand	366-370	5	3
α-helix	375-378	4
β-strand	381-383	3	5
α-helix	385-387	3
β-strand	396-399	4	6
β-strand	408-413	6	6
β-strand	416-420	5	6
β-strand	422-424	3	7
β-strand	433-435	3	7
β-strand	439-440	2	6
α-helix	445-447	3
α-helix	448	1
β-strand	449	1	8
β-strand	452-454	3	9
α-helix	456-458	3
β-strand	464-467	4	9
β-strand	472	1	8
β-strand	476	1	10
β-strand	485-488	4	9
α-helix	494-496	3
α-helix	501-507	7
β-strand	511-516	6	11
β-strand	522-526	5	11
β-strand	527	1	10
α-helix	528-529	2
β-strand	539-541	3	12
β-strand	544-546	3	12
α-helix	547-548	2
β-strand	556-559	4	11
β-strand	570-573	4	11
β-strand	578-581	4	11
β-strand	583	1	13
β-strand	589	1	13
β-strand	593-595	3	11
α-helix	607-609	3
β-strand	610-613	4	14
α-helix	621	1
β-strand	622-626	5	14
β-strand	630-634	5	14
β-strand	636	1	15
β-strand	642	1	15
β-strand	646-649	4	14
α-helix	650	1
β-strand	661-665	5	5
β-strand	674-678	5	5
β-strand	686-689	4	5
β-strand	699-703	5	3
β-strand	708-716	9	3
α-helix	717-730	14
α-helix	735-737	3
β-strand	738	1	3
β-strand	744-753	10	3
β-strand	759-772	14	3
β-strand	777-791	15	3
α-helix	792-793	2
α-helix	800-803	4
β-strand	804-810	7	3
α-helix	815-821	7
α-helix	826-827	2
α-helix	832-835	4
β-strand	838-843	6	3
β-strand	846-849	4	3
α-helix	855-864	10
β-strand	869-876	8	3
β-strand	888-900	13	3
β-strand	908-920	13	3
β-strand	929-938	10	3
β-strand	944-951	8	3
α-helix	952-957	6
α-helix	968	1
α-helix	971-974	4
α-helix	978-980	3
β-strand	982-996	15	3
β-strand	1001-1017	17	3
α-helix	1018-1020	3
α-helix	1028-1031	4
β-strand	1045-1055	11	3
α-helix	1062-1063	2
β-strand	1071-1080	10	3
α-helix	1082-1085	4
α-helix	1086-1088	3
α-helix	1094-1096	3
α-helix	1097-1104	8
β-strand	1107-1110	4	3
α-helix	1111	1
α-helix	1114-1115	2
β-strand	1120-1131	12	3
α-helix	1134-1136	3
β-strand	1140-1146	7	3
α-helix	1150-1151	2
β-strand	1152-1156	5	3
β-strand	1163-1167	5	3
β-strand	1173-1179	7	3
β-strand	1184-1189	6	3
β-strand	1195-1200	6	3
β-strand	1206-1215	10	3
β-strand	1218-1221	4	3
α-helix	1223-1224	2
α-helix	1236-1240	5
β-strand	1250-1255	6	3
α-helix	1257-1259	3
β-strand	1262	1	16
α-helix	1265-1270	6
α-helix	1274-1281	8
β-strand	1285	1	17
β-strand	1290	1	16
β-strand	1291	1	17
α-helix	1293-1300	8
β-strand	1322-1328	7	3
β-strand	1339-1346	8	3
β-strand	1352-1359	8	3
β-strand	1362-1364	3	18
β-strand	1365	1	3
β-strand	1366-1367	2	18
β-strand	1373-1380	8	18
β-strand	1383-1387	5	3
β-strand	1390-1392	3	19
β-strand	1398-1402	5	19
α-helix	1403-1404	2
β-strand	1405-1407	3	3
α-helix	1412-1414	3
α-helix	1415-1419	5
β-strand	1426-1431	6	19
β-strand	1437-1441	5	19
β-strand	1447-1453	7	19
β-strand	1456-1460	5	19
α-helix	1462-1466	5
β-strand	1493-1497	5	19
β-strand	1503-1510	8	19
α-helix	1517-1518	2
β-strand	1519-1527	9	19
β-strand	1533-1537	5	19
α-helix	1539-1545	7
α-helix	1551-1553	3
β-strand	1555-1559	5	19
β-strand	1565-1570	6	19
β-strand	1574-1580	7	19
β-strand	1586-1590	5	19
β-strand	1596-1601	6	19
β-strand	1610-1616	7	19
β-strand	1624-1631	8	19
α-helix	1636-1641	6
β-strand	1647-1651	5	19
β-strand	1655-1662	8	19
β-strand	1668-1676	9	19
α-helix	1689-1693	5
β-strand	1696-1707	12	19
β-strand	1713-1717	5	19
β-strand	1723-1728	6	19
β-strand	1734-1740	7	19
β-strand	1747-1755	9	19
β-strand	1761-1766	6	19
β-strand	1771-1777	7	19
β-strand	1782-1790	9	19
β-strand	1795-1804	10	19
β-strand	1810-1815	6	19
α-helix	1818-1820	3
β-strand	1823	1	20
α-helix	1830-1831	2
β-strand	1832-1833	2	19
β-strand	1834-1836	3	21
β-strand	1842-1850	9	21
α-helix	1851-1853	3
α-helix	1860-1863	4
β-strand	1864	1	22
β-strand	1870	1	20
β-strand	1872-1881	10	21
β-strand	1887-1893	7	21
β-strand	1901-1904	4	21
β-strand	1905-1907	3	23
α-helix	1908	1
β-strand	1914-1916	3	23
α-helix	1923-1925	3
α-helix	1927-1929	3
β-strand	1930	1	24
β-strand	1935	1	25
β-strand	1936	1	24
β-strand	1938-1940	3	26
β-strand	1943-1944	2	26
β-strand	1945-1947	3	22
β-strand	1953-1959	7	22
α-helix	1965-1967	3
β-strand	1968-1974	7	22
β-strand	1980-1987	8	22
β-strand	1994-2001	8	22
β-strand	2004-2010	7	22
β-strand	2017-2024	8	22
β-strand	2032-2039	8	22
β-strand	2049-2055	7	22
β-strand	2061-2065	5	22
β-strand	2071-2077	7	22
β-strand	2083-2088	6	22
α-helix	2091-2094	4
β-strand	2099-2101	3	27
β-strand	2104-2106	3	27
β-strand	2112-2113	2	27
β-strand	2118-2120	3	27
β-strand	2125-2126	2	27
β-strand	2128	1	25
α-helix	2134-2136	3
α-helix	2144-2146	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdB2,TccC3	A	protein	2157	Photorhabdus luminescens	Q8GF97 (AlphaFold model), Q8GF99

Sequence of entity 1 (A), FASTA

>6H6G_1 TcdB2,TccC3 (chains A)
MQNSQDFSITELSLPKGGGAITGMGEALTPTGPDGMAALSLPLPISAGRGYAPAFTLNYN
SGAGNSPFGLGWDCNVMTIRRRTHFGVPHYDETDTFLGPEGEVLVVADQPRDESTLQGIN
LGATFTVTGYRSRLESHFSRLEYWQPKTTGKTDFWLIYSPDGQVHLLGKSPQARISNPSQ
TTQTAQWLLEASVSSRGEQIYYQYRAEDDTGCEADEITHHLQATAQRYLHIVYYGNRTAS
ETLPGLDGSAPSQADWLFYLVFDYGERSNNLKTPPAFSTTGSWLCRQDRFSRYEYGFEIR
TRRLCRQVLMYHHLQALDSKITEHNGPTLVSRLILNYDESAIASTLVFVRRVGHEQDGNV
VTLPPLELAYQDFSPRHHAHWQPMDVLANFNAIQRWQLVDLKGEGLPGLLYQDKGAWWYR
SAQRLGEIGSDAVTWEKMQPLSVIPSLQSNASLVDINGDGQLDWVITGPGLRGYHSQRPD
GSWTRFTPLNALPVEYTHPRAQLADLMGAGLSDLVLIGPKSVRLYANTRDGFAKGKDVVQ
SGDITLPVPGADPRKLVAFSDVLGSGQAHLVEVSATKVTCWPNLGRGRFGQPITLPGFSQ
PATEFNPAQVYLADLDGSGPTDLIYVHTNRLDIFLNKSGNGFAEPVTLRFPEGLRFDHTC
QLQMADVQGLGVASLILSVPHMSPHHWRCDLTNMKPWLLNEMNNNMGVHHTLRYRSSSQF
WLDEKAAALTTGQTPVCYLPFPIHTLWQTETEDEISGNKLVTTLRYARGAWDGREREFRG
FGYVEQTDSHQLAQGNAPERTPPALTKNWYATGLPVIDNALSTEYWRDDQAFAGFSPRFT
TWQDNKDVPLTPEDDNSRYWFNRALKGQLLRSELYGLDDSTNKHVPYTVTEFRSQVRRLQ
HTDSRYPVLWSSVVESRNYHYERIASDPQCSQNITLSSDRFGQPLKQLSVQYPRRQQPAI
NLYPDTLPDKLLANSYDDQQRQLRLTYQQSSWHHLTNNTVRVLGLPDSTRSDIFTYGAEN
VPAGGLNLELLSDKNSLIADDKPREYLGQQKTAYTDGQNTTPLQTPTRQALIAFTETTVF
NQSTLSAFNGSIPSDKLSTTLEQAGYQQTNYLFPRTGEDKVWVAHHGYTDYGTAAQFWRP
QKQSNTQLTGKITLIWDANYCVVVQTRDAAGLTTSAKYDWRFLTPVQLTDINDNQHLITL
DALGRPITLRFWGTENGKMTGYSSPEKASFSPPSDVNAAIELKKPLPVAQCQVYAPESWM
PVLSQKTFNRLAEQDWQKLYNARIITEDGRICTLAYRRWVQSQKAIPQLISLLNNGPRLP
PHSLTLTTDRYDHDPEQQIRQQVVFSDGFGRLLQAAARHEAGMARQRNEDGSLIINVQHT
ENRWAVTGRTEYDNKGQPIRTYQPYFLNDWRYVSNDSARQEKEAYADTHVYDPIGREIKV
ITAKGWFRRTLFTPWFTVNEDENDTAAEVKKVKMPGSRPMKNIDPKLYQKTPTVSVYDNR
GLIIRNIDFHRTTANGDPDTRITRHQYDIHGHLNQSIDPRLYEAKQTNNTIKPNFLWQYD
LTGNPLCTESIDAGRTVTLNDIEGRPLLTVTATGVIQTRQYETSSLPGRLLSVAEQTPEE
KTSRITERLIWAGNTEAEKDHNLAGQCVRHYDTAGVTRLESLSLTGTVLSQSSQLLIDTQ
EANWTGDNETVWQNMLADDIYTTLSTFDATGALLTQTDAKGNIQRLAYDVAGQLNGSWLT
LKGQTEQVIIKSLTYSAAGQKLREEHGNDVITEYSYEPETQRLIGIKTRRPSDTKVLQDL
RYEYDPVGNVISIRNDAEATRFWHNQKVMPENTYTYDSLYQLISATGREMANIGQQSHQF
PSPALPSDNNTYTNYTRTYTYDRGGNLTKIQHSSPATQNNYTTNITVSNRSNRAVLSTLT
EDPAQVDALFDAGGHQNTLISGQNLNWNTRGELQQVTLVKRDKGANDDREWYRYSGDGRR
MLKINEQQASNNAQTQRVTYLPNLELRLTQNSTATTEDLQVITVGEAGRAQVRVLHWESG
KPEDIDNNQLRYSYDNLIGSSQLELDSEGQIISEEEYYPYGGTALWAARNQTEASYKTIR
YSGKERDATGLYYYGYRYYQPWIGRWLSSDPAGTIDGLNLYRMVRNNPVTLLDPDGL

Primary citation

Tc toxin activation requires unfolding and refolding of a beta-propeller. Gatsogiannis, C., Merino, F., Roderer, D. et al. Nature (2018) 563:209-213. DOI 10.1038/s41586-018-0556-6 · PubMed

Other PDB entries of the same protein (UniProt Q8GF97 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
4O9X 2.17 Å, Crystal Structure of TcdB2-TccC3
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
6SUQ 3.7 Å, Crystal Structure of TcdB2-TccC3-TEV
6H6F 3.72 Å, PTC3 holotoxin complex from Photorhabdus luminiscens - Mutant TcC-D651A
7Z7H 3.8 Å, Structure of P. luminescens TccC3-F-actin complex
6H6E 3.95 Å, PTC3 holotoxin complex from Photorhabdus luminecens in prepore state (TcdA1, TcdB2, TccC3)
7ZBQ Structure of the ADP-ribosyltransferase TccC3HVR from Photorhabdus Luminescens

Browse structure collections

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