4O9X: TcdB2-TccC3

Name: PDB 4O9X: Crystal Structure of TcdB2-TccC3
Published: 2014-02-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal Structure of TcdB2-TccC3. Determined by X-ray diffraction at 2.17 Å resolution. Released 26 Feb 2014.

Method: X-ray diffraction
Resolution: 2.17 Å
Organism: Photorhabdus luminescens
Chains: 1
Atoms: 17,581
Mol. weight: 249.13 kDa
Ligands: HG
Released: 26 Feb 2014

Explore 4O9X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O9X contains 75 α-helices and 164 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: 75 helices, 164 β-strands

Element	Residues	Length	Sheet
α-helix	48-50	3
β-strand	61-62	2	1
β-strand	72-76	5	1
β-strand	90-94	5	1
β-strand	106-107	2	1
β-strand	112-115	4	2
β-strand	130-131	2	2
α-helix	136	1
β-strand	137	1	2
β-strand	138-140	3	3
β-strand	145-150	6	3
β-strand	153-166	14	3
β-strand	168-169	2	3
β-strand	174-180	7	3
β-strand	188-192	5	3
β-strand	195	1	3
β-strand	198-201	4	3
α-helix	205-207	3
β-strand	208-211	4	2
β-strand	214-222	9	2
β-strand	223-227	5	3
β-strand	233-240	8	3
α-helix	248-253	6
β-strand	261-270	10	3
α-helix	277	1
α-helix	283-285	3
α-helix	287-289	3
β-strand	290-297	8	3
α-helix	308-310	3
α-helix	315-320	6
β-strand	324-326	3	4
β-strand	333-335	3	4
β-strand	341-346	6	3
α-helix	348-351	4
β-strand	362-372	11	3
β-strand	379-388	10	3
β-strand	394-396	3	3
α-helix	397-399	3
β-strand	400-404	5	3
α-helix	409-412	4
β-strand	416-417	2	5
α-helix	419-421	3
β-strand	430-433	4	6
β-strand	442-447	6	6
β-strand	450-454	5	6
β-strand	456-458	3	7
β-strand	467-469	3	7
β-strand	473-474	2	6
α-helix	479-481	3
α-helix	483	1
β-strand	485-488	4	8
β-strand	498-501	4	8
β-strand	519-522	4	8
α-helix	523-525	3
α-helix	528-530	3
α-helix	535-541	7
β-strand	545-552	8	9
β-strand	555-560	6	9
α-helix	561	1
α-helix	563	1
β-strand	572-575	4	10
β-strand	578-581	4	10
β-strand	590-594	5	9
β-strand	603-607	5	9
β-strand	612-615	4	9
β-strand	617-619	3	11
β-strand	622-623	2	11
β-strand	627-628	2	9
α-helix	641-643	3
β-strand	644-647	4	12
α-helix	655	1
β-strand	656-660	5	12
β-strand	664-668	5	12
β-strand	670	1	13
β-strand	676	1	13
α-helix	677	1
α-helix	679	1
β-strand	680-683	4	12
α-helix	684	1
β-strand	695-699	5	5
α-helix	707	1
β-strand	708-712	5	5
β-strand	720-723	4	5
β-strand	733-737	5	3
β-strand	742-750	9	3
α-helix	751-764	14
α-helix	769-771	3
β-strand	778-787	10	3
β-strand	793-806	14	3
β-strand	811-825	15	3
α-helix	826-827	2
α-helix	835-837	3
β-strand	838-844	7	3
α-helix	849-855	7
α-helix	856-858	3
α-helix	860-861	2
α-helix	866-869	4
β-strand	872-877	6	3
β-strand	880-883	4	3
α-helix	889-897	9
β-strand	903-910	8	3
β-strand	922-934	13	3
β-strand	942-954	13	3
β-strand	963-972	10	3
β-strand	978-985	8	3
α-helix	986-992	7
α-helix	1002	1
α-helix	1007-1009	3
α-helix	1012-1014	3
β-strand	1016-1031	16	3
β-strand	1034-1051	18	3
α-helix	1052-1054	3
α-helix	1062-1066	5
β-strand	1079-1089	11	3
α-helix	1096-1097	2
β-strand	1105-1114	10	3
α-helix	1116-1119	4
α-helix	1120-1122	3
α-helix	1128-1130	3
α-helix	1131-1137	7
β-strand	1141-1144	4	3
α-helix	1145	1
β-strand	1154-1160	7	3
β-strand	1162-1165	4	14
α-helix	1168-1170	3
β-strand	1174-1178	5	14
α-helix	1184-1185	2
β-strand	1186-1190	5	14
β-strand	1197-1201	5	14
β-strand	1207-1213	7	14
β-strand	1218-1223	6	14
β-strand	1229-1234	6	14
β-strand	1240-1249	10	14
β-strand	1252-1255	4	14
α-helix	1257-1258	2
α-helix	1265-1267	3
α-helix	1270-1274	5
β-strand	1284-1289	6	14
β-strand	1356-1362	7	14
β-strand	1373-1380	8	14
β-strand	1386-1392	7	14
β-strand	1396-1398	3	15
β-strand	1399	1	14
β-strand	1400-1401	2	15
β-strand	1407-1414	8	15
β-strand	1418-1421	4	14
β-strand	1424-1426	3	16
β-strand	1432-1436	5	16
β-strand	1439-1441	3	14
α-helix	1446-1448	3
α-helix	1449-1454	6
α-helix	1456-1458	3
β-strand	1460-1465	6	16
β-strand	1471-1475	5	16
β-strand	1481-1486	6	16
β-strand	1490-1494	5	16
α-helix	1500-1502	3
α-helix	1519-1521	3
β-strand	1527-1531	5	16
β-strand	1537-1544	8	16
α-helix	1551-1552	2
β-strand	1553-1561	9	16
β-strand	1567-1571	5	16
α-helix	1573-1579	7
α-helix	1585-1587	3
β-strand	1589-1593	5	16
β-strand	1599-1604	6	16
β-strand	1608-1614	7	16
β-strand	1620-1624	5	16
β-strand	1630-1635	6	16
β-strand	1644-1650	7	16
β-strand	1658-1665	8	16
α-helix	1670-1674	5
β-strand	1681-1685	5	16
β-strand	1689-1696	8	16
β-strand	1702-1709	8	16
β-strand	1710	1	17
α-helix	1711	1
α-helix	1723-1728	6
β-strand	1730	1	17
β-strand	1735-1741	7	16
β-strand	1747-1751	5	16
β-strand	1757-1762	6	16
β-strand	1768-1774	7	16
β-strand	1781-1789	9	16
β-strand	1795-1800	6	16
β-strand	1805-1811	7	16
β-strand	1816-1824	9	16
β-strand	1829-1838	10	16
β-strand	1844-1849	6	16
α-helix	1852-1854	3
β-strand	1857	1	18
α-helix	1862-1865	4
β-strand	1866-1867	2	16
β-strand	1868-1870	3	19
β-strand	1876-1884	9	19
α-helix	1895-1897	3
β-strand	1898	1	20
α-helix	1900-1902	3
β-strand	1904	1	18
β-strand	1906-1915	10	19
β-strand	1921-1927	7	19
α-helix	1929-1931	3
β-strand	1935-1938	4	19
β-strand	1939-1941	3	21
α-helix	1942	1
β-strand	1948-1950	3	21
α-helix	1957-1959	3
α-helix	1961-1963	3
β-strand	1964	1	22
β-strand	1969	1	23
β-strand	1970	1	22
β-strand	1972	1	24
β-strand	1978	1	24
β-strand	1979-1981	3	20
β-strand	1987-1993	7	20
β-strand	2002-2008	7	20
β-strand	2014-2023	10	20
β-strand	2026-2035	10	20
β-strand	2038-2045	8	20
β-strand	2048-2058	11	20
β-strand	2066-2073	8	20
α-helix	2080	1
β-strand	2083-2089	7	20
β-strand	2095-2099	5	20
β-strand	2105-2111	7	20
β-strand	2117-2122	6	20
α-helix	2125-2128	4
β-strand	2133	1	25
α-helix	2135-2137	3
β-strand	2139-2140	2	25
β-strand	2146-2148	3	25
β-strand	2151-2154	4	25
β-strand	2159-2160	2	25
β-strand	2162	1	23
β-strand	2169	1	26
β-strand	2171	1	26
β-strand	2176	1	25
α-helix	2178-2180	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdB2, TccC3	A	protein	2191	Photorhabdus luminescens	Q8GF97 (AlphaFold model), Q8GF99

Sequence of entity 1 (A), FASTA

>4O9X_1 TcdB2, TccC3 (chains A)
MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSMQNSQDFSITELSLPKGGGAITGMGE
ALTPTGPDGMAALSLPLPISAGRGYAPAFTLNYNSGAGNSPFGLGWDCNVMTIRRRTHFG
VPHYDETDTFLGPEGEVLVVADQPRDESTLQGINLGATFTVTGYRSRLESHFSRLEYWQP
KTTGKTDFWLIYSPDGQVHLLGKSPQARISNPSQTTQTAQWLLEASVSSRGEQIYYQYRA
EDDTGCEADEITHHLQATAQRYLHIVYYGNRTASETLPGLDGSAPSQADWLFYLVFDYGE
RSNNLKTPPAFSTTGSWLCRQDRFSRYEYGFEIRTRRLCRQVLMYHHLQALDSKITEHNG
PTLVSRLILNYDESAIASTLVFVRRVGHEQDGNVVTLPPLELAYQDFSPRHHAHWQPMDV
LANFNAIQRWQLVDLKGEGLPGLLYQDKGAWWYRSAQRLGEIGSDAVTWEKMQPLSVIPS
LQSNASLVDINGDGQLDWVITGPGLRGYHSQRPDGSWTRFTPLNALPVEYTHPRAQLADL
MGAGLSDLVLIGPKSVRLYANTRDGFAKGKDVVQSGDITLPVPGADPRKLVAFSDVLGSG
QAHLVEVSATKVTCWPNLGRGRFGQPITLPGFSQPATEFNPAQVYLADLDGSGPTDLIYV
HTNRLDIFLNKSGNGFAEPVTLRFPEGLRFDHTCQLQMADVQGLGVASLILSVPHMSPHH
WRCDLTNMKPWLLNEMNNNMGVHHTLRYRSSSQFWLDEKAAALTTGQTPVCYLPFPIHTL
WQTETEDEISGNKLVTTLRYARGAWDGREREFRGFGYVEQTDSHQLAQGNAPERTPPALT
KNWYATGLPVIDNALSTEYWRDDQAFAGFSPRFTTWQDNKDVPLTPEDDNSRYWFNRALK
GQLLRSELYGLDDSTNKHVPYTVTEFRSQVRRLQHTDSRYPVLWSSVVESRNYHYERIAS
DPQCSQNITLSSDRFGQPLKQLSVQYPRRQQPAINLYPDTLPDKLLANSYDDQQRQLRLT
YQQSSWHHLTNNTVRVLGLPDSTRSDIFTYGAENVPAGGLNLELLSDKNSLIADDKPREY
LGQQKTAYTDGQNTTPLQTPTRQALIAFTETTVFNQSTLSAFNGSIPSDKLSTTLEQAGY
QQTNYLFPRTGEDKVWVAHHGYTDYGTAAQFWRPQKQSNTQLTGKITLIWDANYCVVVQT
RDAAGLTTSAKYDWRFLTPVQLTDINDNQHLITLDALGRPITLRFWGTENGKMTGYSSPE
KASFSPPSDVNAAIELKKPLPVAQCQVYAPESWMPVLSQKTFNRLAEQDWQKLYNARIIT
EDGRICTLAYRRWVQSQKAIPQLISLLNNGPRLPPHSLTLTTDRYDHDPEQQIRQQVVFS
DGFGRLLQAAARHEAGMARQRNEDGSLIINVQHTENRWAVTGRTEYDNKGQPIRTYQPYF
LNDWRYVSNDSARQEKEAYADTHVYDPIGREIKVITAKGWFRRTLFTPWFTVNEDENDTA
AEVKKVKMPGSRPMKNIDPKLYQKTPTVSVYDNRGLIIRNIDFHRTTANGDPDTRITRHQ
YDIHGHLNQSIDPRLYEAKQTNNTIKPNFLWQYDLTGNPLCTESIDAGRTVTLNDIEGRP
LLTVTATGVIQTRQYETSSLPGRLLSVAEQTPEEKTSRITERLIWAGNTEAEKDHNLAGQ
CVRHYDTAGVTRLESLSLTGTVLSQSSQLLIDTQEANWTGDNETVWQNMLADDIYTTLST
FDATGALLTQTDAKGNIQRLAYDVAGQLNGSWLTLKGQTEQVIIKSLTYSAAGQKLREEH
GNDVITEYSYEPETQRLIGIKTRRPSDTKVLQDLRYEYDPVGNVISIRNDAEATRFWHNQ
KVMPENTYTYDSLYQLISATGREMANIGQQSHQFPSPALPSDNNTYTNYTRTYTYDRGGN
LTKIQHSSPATQNNYTTNITVSNRSNRAVLSTLTEDPAQVDALFDAGGHQNTLISGQNLN
WNTRGELQQVTLVKRDKGANDDREWYRYSGDGRRMLKINEQQASNNAQTQRVTYLPNLEL
RLTQNSTATTEDLQVITVGEAGRAQVRVLHWESGKPEDIDNNQLRYSYDNLIGSSQLELD
SEGQIISEEEYYPYGGTALWAARNQTEASYKTIRYSGKERDATGLYYYGYRYYQPWIGRW
LSSDPAGTIDGLNLYRMVRNNPVTLLDPDGL

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	9

Primary citation

Mechanism of Tc toxin action revealed in molecular detail. Meusch, D., Gatsogiannis, C., Efremov, R.G. et al. Nature (2014) 508:61-65. DOI 10.1038/nature13015 · 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
6H6G 3.0 Å, Crystal Structure of TcdB2-TccC3 without hypervariable C-terminal region
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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