5LKI: Tc toxin TcdA1 in its pore state

Name: PDB 5LKI: Cryo-EM structure of the Tc toxin TcdA1 in its pore state
Published: 2016-08-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cryo-EM structure of the Tc toxin TcdA1 in its pore state. Determined by electron microscopy at 3.46 Å resolution. Released 31 Aug 2016.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Photorhabdus luminescens
Chains: 5
Atoms: 55,415
Mol. weight: 1416.15 kDa
Released: 31 Aug 2016

Explore 5LKI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LKI contains 265 α-helices and 267 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 and E: 53 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	111	1	1
α-helix	115-126	12
α-helix	138-141	4
α-helix	143-145	3
β-strand	149	1	2
α-helix	152-156	5
β-strand	159-160	2	3
α-helix	164-175	12
α-helix	182-189	8
α-helix	202-213	12
α-helix	891-897	7
α-helix	912-924	13
α-helix	928-952	25
α-helix	964-970	7
β-strand	982-983	2	3
α-helix	985-1002	18
α-helix	1016-1019	4
α-helix	1021-1025	5
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1055-1065	11
α-helix	1071-1088	18
β-strand	1092-1098	7	4
β-strand	1107-1113	7	4
β-strand	1122-1123	2	4
β-strand	1125-1127	3	4
β-strand	1141	1	4
α-helix	1142-1144	3
β-strand	1145-1146	2	4
α-helix	1147	1
β-strand	1159-1163	5	5
β-strand	1166-1171	6	5
β-strand	1197-1202	6	5
β-strand	1203	1	6
α-helix	1208	1
β-strand	1209	1	6
α-helix	1210-1211	2
β-strand	1213-1216	4	5
α-helix	1218-1222	5
β-strand	1235-1238	4	7
β-strand	1245-1249	5	7
β-strand	1265-1269	5	7
β-strand	1275-1277	3	7
α-helix	1278-1279	2
α-helix	1280-1290	11
β-strand	1303	1	4
β-strand	1587-1588	2	8
β-strand	1594-1596	3	8
β-strand	1603-1604	2	8
α-helix	1610-1619	10
α-helix	1621-1624	4
β-strand	1633-1635	3	9
β-strand	1641-1646	6	10
β-strand	1660-1663	4	11
α-helix	1668-1670	3
β-strand	1677-1680	4	11
β-strand	1688-1692	5	10
β-strand	1705-1706	2	12
β-strand	1709-1710	2	11
β-strand	1724-1725	2	12
β-strand	1735	1	12
β-strand	1746-1749	4	10
β-strand	1755-1757	3	9
α-helix	1758-1759	2
α-helix	1765-1768	4
α-helix	1769-1774	6
α-helix	1775-1786	12
α-helix	1789-1797	9
β-strand	1800	1	13
β-strand	1805	1	14
β-strand	1812	1	14
β-strand	1816	1	13
α-helix	1819-1822	4
α-helix	1846-1868	23
α-helix	1873-1890	18
α-helix	1893-1894	2
β-strand	1906	1	2
α-helix	1907-1910	4
β-strand	1949	1	1
α-helix	1954-1971	18
α-helix	1987-1991	5
α-helix	1992-2004	13
β-strand	2017	1	15
α-helix	2019-2102	84
α-helix	2109-2139	31
α-helix	2154-2243	90
α-helix	2248-2283	36
α-helix	2300-2303	4
α-helix	2307-2324	18
β-strand	2330-2336	7	16
α-helix	2337-2343	7
α-helix	2346-2348	3
α-helix	2353-2362	10
β-strand	2375-2377	3	17
β-strand	2387-2392	6	17
α-helix	2398-2400	3
β-strand	2410-2418	9	16
β-strand	2431-2433	3	17
β-strand	2449-2450	2	17
β-strand	2456	1	16
β-strand	2468	1	15
α-helix	2469-2470	2
β-strand	2476	1	16
β-strand	2481-2486	6	17
α-helix	2498-2503	6
β-strand	2508-2515	8	16

Chain D: 53 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	111	1	52
α-helix	115-126	12
α-helix	138-141	4
α-helix	143-145	3
β-strand	149	1	53
α-helix	152-156	5
β-strand	159-160	2	54
α-helix	164-175	12
α-helix	182-189	8
α-helix	202-213	12
α-helix	891-897	7
α-helix	912-924	13
α-helix	928-952	25
α-helix	964-970	7
β-strand	982-983	2	54
α-helix	985-1002	18
α-helix	1016-1019	4
α-helix	1021-1025	5
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1055-1065	11
α-helix	1071-1088	18
β-strand	1092-1098	7	55
β-strand	1107-1113	7	55
β-strand	1122-1123	2	55
β-strand	1125-1127	3	55
β-strand	1141	1	55
α-helix	1142-1144	3
β-strand	1145-1146	2	55
α-helix	1147	1
β-strand	1159-1163	5	56
β-strand	1166-1171	6	56
β-strand	1197-1202	6	56
β-strand	1203	1	57
α-helix	1208	1
β-strand	1209	1	57
α-helix	1210-1211	2
β-strand	1213-1216	4	56
α-helix	1218-1222	5
β-strand	1235-1238	4	58
β-strand	1245-1249	5	58
β-strand	1265-1269	5	58
β-strand	1275-1277	3	58
α-helix	1278-1279	2
α-helix	1280-1290	11
β-strand	1303	1	55
β-strand	1587-1588	2	59
β-strand	1594-1596	3	59
β-strand	1603-1604	2	59
α-helix	1610-1619	10
α-helix	1621-1624	4
β-strand	1633-1635	3	60
β-strand	1639	1	61
β-strand	1641-1646	6	62
β-strand	1660-1663	4	63
α-helix	1668-1670	3
β-strand	1677-1680	4	63
β-strand	1688-1692	5	62
β-strand	1694	1	61
β-strand	1705-1706	2	64
β-strand	1709-1710	2	63
β-strand	1724-1725	2	64
β-strand	1735	1	64
β-strand	1746-1749	4	62
β-strand	1755-1757	3	60
α-helix	1758-1759	2
α-helix	1765-1768	4
α-helix	1769-1774	6
α-helix	1775-1786	12
α-helix	1789-1797	9
β-strand	1800	1	65
β-strand	1805	1	66
β-strand	1812	1	66
β-strand	1816	1	65
α-helix	1819-1822	4
α-helix	1846-1868	23
α-helix	1873-1890	18
α-helix	1893-1894	2
β-strand	1906	1	53
α-helix	1907-1910	4
β-strand	1949	1	52
α-helix	1954-1971	18
α-helix	1987-1991	5
α-helix	1992-2004	13
β-strand	2017	1	67
α-helix	2019-2102	84
α-helix	2109-2139	31
α-helix	2154-2243	90
α-helix	2248-2283	36
α-helix	2300-2303	4
α-helix	2307-2324	18
β-strand	2330-2336	7	68
α-helix	2337-2343	7
α-helix	2346-2348	3
α-helix	2353-2362	10
β-strand	2375-2377	3	69
β-strand	2387-2392	6	69
α-helix	2398-2400	3
β-strand	2410-2418	9	68
β-strand	2431-2433	3	69
β-strand	2449-2450	2	69
β-strand	2456	1	68
β-strand	2468	1	67
α-helix	2469-2470	2
β-strand	2476	1	68
β-strand	2481-2486	6	69
α-helix	2498-2503	6
β-strand	2508-2515	8	68

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

>5LKI_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

Membrane insertion of a Tc toxin in near-atomic detail. Gatsogiannis, C., Merino, F., Prumbaum, D. et al. Nat Struct Mol Biol (2016) 23:884-890. DOI 10.1038/nsmb.3281 · PubMed

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
6L7E 3.2 Å, Toxin Complex TcdA1-TcdB1-TccC2
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)
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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