6SUP: TcdB2-TccC3-Cdc42

Name: PDB 6SUP: Crystal Structure of TcdB2-TccC3-Cdc42
Published: 2019-12-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal Structure of TcdB2-TccC3-Cdc42. Determined by X-ray diffraction at 2.0 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Photorhabdus luminescens, Homo sapiens
Chains: 1
Atoms: 18,283
Mol. weight: 240.9 kDa
Ligands: MG
Released: 4 Dec 2019

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

Secondary structure: helices and β-sheets

6SUP contains 73 α-helices and 166 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: 73 helices, 166 β-strands

Element	Residues	Length	Sheet
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	174-177	4	2
β-strand	180-188	9	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	243	1
α-helix	249-251	3
α-helix	253-255	3
β-strand	256-263	8	3
α-helix	274-276	3
α-helix	281-284	4
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
α-helix	364-365	2
β-strand	366-370	5	3
α-helix	375-378	4
β-strand	382-383	2	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
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	485-488	4	9
α-helix	489-491	3
α-helix	501-506	6
β-strand	511-518	8	10
β-strand	521-526	6	10
α-helix	527	1
β-strand	538-541	4	11
β-strand	544-547	4	11
α-helix	548	1
β-strand	556-559	4	10
β-strand	570-573	4	10
β-strand	578-581	4	10
β-strand	583-585	3	12
β-strand	588-589	2	12
β-strand	593-594	2	10
α-helix	607-609	3
β-strand	610-613	4	13
α-helix	621	1
β-strand	622-626	5	13
β-strand	630-634	5	13
β-strand	636	1	14
β-strand	642	1	14
α-helix	643	1
α-helix	645	1
β-strand	646-649	4	13
α-helix	650	1
β-strand	661-665	5	5
α-helix	673	1
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
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	815-818	4
α-helix	821-824	4
α-helix	826-827	2
α-helix	832-835	4
β-strand	838-843	6	3
β-strand	846-849	4	3
α-helix	855-863	9
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	952-958	7
α-helix	968	1
α-helix	971-974	4
α-helix	978-981	4
β-strand	982-997	16	3
β-strand	1000-1017	18	3
α-helix	1018-1020	3
α-helix	1028-1032	5
β-strand	1045-1055	11	3
α-helix	1062-1063	2
β-strand	1071-1080	10	3
α-helix	1084-1088	5
α-helix	1094-1103	10
β-strand	1107-1110	4	3
α-helix	1111	1
β-strand	1120-1126	7	3
β-strand	1128-1131	4	15
α-helix	1134-1136	3
β-strand	1140-1144	5	15
α-helix	1150-1151	2
β-strand	1152-1156	5	15
β-strand	1163-1167	5	15
β-strand	1173-1179	7	15
β-strand	1184-1189	6	15
β-strand	1195-1200	6	15
β-strand	1206-1215	10	15
β-strand	1218-1221	4	15
α-helix	1223-1224	2
α-helix	1236-1240	5
β-strand	1250-1255	6	15
β-strand	1262	1	16
α-helix	1265-1270	6
α-helix	1276-1280	5
β-strand	1285	1	17
β-strand	1290	1	16
β-strand	1291	1	17
α-helix	1293-1300	8
α-helix	1307-1312	6
β-strand	1322-1328	7	15
β-strand	1339-1346	8	15
β-strand	1352-1358	7	15
β-strand	1362-1364	3	18
β-strand	1365	1	15
β-strand	1366-1367	2	18
β-strand	1373-1380	8	18
β-strand	1384-1387	4	15
β-strand	1390-1392	3	19
β-strand	1398-1402	5	19
β-strand	1405-1407	3	15
α-helix	1412-1414	3
α-helix	1415-1420	6
β-strand	1426-1431	6	19
β-strand	1437-1441	5	19
β-strand	1447-1452	6	19
β-strand	1456-1460	5	19
α-helix	1466-1468	3
α-helix	1485-1487	3
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	1539-1547	9
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	1636-1639	4
β-strand	1647-1651	5	19
β-strand	1655-1662	8	19
β-strand	1668-1675	8	19
β-strand	1676	1	20
α-helix	1677	1
α-helix	1689-1693	5
β-strand	1696	1	20
β-strand	1701-1707	7	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	1771-1776	6	19
β-strand	1783-1790	8	19
β-strand	1795-1804	10	19
β-strand	1810-1815	6	19
α-helix	1818-1820	3
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	1861-1863	3
β-strand	1864	1	22
α-helix	1865	1
β-strand	1872-1881	10	21
β-strand	1887-1893	7	21
β-strand	1900-1904	5	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	1	26
β-strand	1944	1	26
β-strand	1945-1947	3	22
β-strand	1953-1959	7	22
α-helix	1966-1967	2
β-strand	1968-1974	7	22
β-strand	1980-1987	8	22
β-strand	1994-2001	8	22
β-strand	2004-2011	8	22
β-strand	2017-2024	8	22
β-strand	2032-2039	8	22
α-helix	2046	1
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	1	27
α-helix	2101-2103	3
β-strand	2105-2106	2	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	2133-2136	4
β-strand	2142	1	27
α-helix	2144-2146	3
α-helix	2331-2338	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdB2,TccC3,Cell division control protein 42 homolog	A	protein	2128	Photorhabdus luminescens, Homo sapiens	P60953 (AlphaFold model), Q8GF97 (AlphaFold model), Q8GF99

Sequence of entity 1 (A), FASTA

>6SUP_1 TcdB2,TccC3,Cell division control protein 42 homolog (chains A)
GPDGMAALSLPLPISAGRGYAPAFTLNYNSGAGNSPFGLGWDCNVMTIRRRTHFGVPHYD
ETDTFLGPEGEVLVVADQPRDESTLQGINLGATFTVTGYRSRLESHFSRLEYWQPKTTGK
TDFWLIYSPDGQVHLLGKSPQARISNPSQTTQTAQWLLEASVSSRGEQIYYQYRAEDDTG
CEADEITHHLQATAQRYLHIVYYGNRTASETLPGLDGSAPSQADWLFYLVFDYGERSNNL
KTPPAFSTTGSWLCRQDRFSRYEYGFEIRTRRLCRQVLMYHHLQALDSKITEHNGPTLVS
RLILNYDESAIASTLVFVRRVGHEQDGNVVTLPPLELAYQDFSPRHHAHWQPMDVLANFN
AIQRWQLVDLKGEGLPGLLYQDKGAWWYRSAQRLGEIGSDAVTWEKMQPLSVIPSLQSNA
SLVDINGDGQLDWVITGPGLRGYHSQRPDGSWTRFTPLNALPVEYTHPRAQLADLMGAGL
SDLVLIGPKSVRLYANTRDGFAKGKDVVQSGDITLPVPGADPRKLVAFSDVLGSGQAHLV
EVSATKVTCWPNLGRGRFGQPITLPGFSQPATEFNPAQVYLADLDGSGPTDLIYVHTNRL
DIFLNKSGNGFAEPVTLRFPEGLRFDHTCQLQMADVQGLGVASLILSVPHMSPHHWRCDL
TNMKPWLLNEMNNNMGVHHTLRYRSSSQFWLDEKAAALTTGQTPVCYLPFPIHTLWQTET
EDEISGNKLVTTLRYARGAWDGREREFRGFGYVEQTDSHQLAQGNAPERTPPALTKNWYA
TGLPVIDNALSTEYWRDDQAFAGFSPRFTTWQDNKDVPLTPEDDNSRYWFNRALKGQLLR
SELYGLDDSTNKHVPYTVTEFRSQVRRLQHTDSRYPVLWSSVVESRNYHYERIASDPQCS
QNITLSSDRFGQPLKQLSVQYPRRQQPAINLYPDTLPDKLLANSYDDQQRQLRLTYQQSS
WHHLTNNTVRVLGLPDSTRSDIFTYVAENVPAGGLNLELLSDKNSLIADDKPREYLGQQK
TAYTDGQNTTPLQTPTRQALIAFTETTVFNQSTLSAFNGSIPSDKLSTTLEQAGYQQTNY
LFPRTGEDKVWVAHHGYTDYGTAAQFWRPQKQSNTQLTGKITLIWDANYCVVVQTRDAAG
LTTSAKYDWRFLTPVQLTDINDNQHLITLDALGRPITLRFWGTENGKMTGYSSPEKASFS
PPSDVNAAIELKKPLPVAQCQVYAPESWMPVLSQKTFNRLAEQDWQKLYNARIITEDGRI
CTLAYRRWVQSQKAIPQLISLLNNGPRLPPHSLTLTTDRYDHDPEQQIRQQVVFSDGFGR
LLQAAARHEAGMARQRNEDGSLIINVQHTENRWAVTGRTEYDNKGQPIRTYQPYFLNDWR
YVSNDSARQEKEAYADTHVYDPIGREIKVITAKGWFRRTLFTPWFTVNEDENDTAAEVKK
IDPKLYQKTPTVSVYDNRGLIIRNIDFHRTTANGDPDTRITRHQYDIHGHLNQSIDPRLY
EAKQTNNTIKPNFLWQYDLTGNPLCTESIDAGRTVTLNDIEGRPLLTVTATGVIQTRQYE
TSSLPGRLLSVAEQTPEEKTSRITERLIWAGNTEAEKDHNLAGQCVRHYDTAGVTRLESL
SLTGTVLSQSSQLLIDTQEANWTGDNETVWQNMLADDIYTTLSTFDATGALLTQTDAKGN
IQRLAYDVAGQLNGSWLTLKGQTEQVIIKSLTYSAAGQKLREEHGNDVITEYSYEPETQR
LIGIKTRRPSDTKVLQDLRYEYDPVGNVISIRNDAEATRFWHNQKVMPENTYTYDSLYQL
ISATGREMANIGQQSHQFPSPALPSDNNTYTNYTRTYTYDRGGNLTKIQHSSPATQNNYT
TNITVSNRSNRAVLSTLTEDPAQVDALFDAGGHQNTLISGQNLNWNTRGELQQVTLVKRD
KGANDDREWYRYSGDGRRMLKINEQQASNNAQTQRVTYLPNLELRLTQNSTATTEDLQVI
TVGEAGRAQVRVLHWESGKPEDIDNNQLRYSYDNLIGSSQLELDSEGQIISEEEYYPYGG
TALWAARNQTEASYKTIRYSGKERDATGLYYYGYRYYQPWIGRWLSSDPAGTIDGLNLYR
MVRNNPVTLLDPDGLNVFDEAILAALEP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

Primary citation

Towards the application of Tc toxins as a universal protein translocation system. Roderer, D., Schubert, E., Sitsel, O. et al. Nat Commun (2019) 10:5263-5263. DOI 10.1038/s41467-019-13253-8 · PubMed

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
1NF3 2.1 Å, Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity…
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex
4ITR 2.3 Å, Crystal Structure of IbpAFic2-H3717A in complex with adenylylated Cdc42

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