8CQ0: TcdA1

Name: PDB 8CQ0: Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567W K2008W mutant
Published: 2024-03-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Photorhabdus luminescens TcdA1 prepore-to-pore intermediate, K567W K2008W mutant. Determined by electron microscopy at 3.2 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Photorhabdus luminescens
Chains: 5
Atoms: 84,445
Mol. weight: 1427.45 kDa
Released: 13 Mar 2024

Explore 8CQ0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CQ0 contains 570 α-helices and 410 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: 114 helices, 82 β-strands

Element	Residues	Length	Sheet
α-helix	92-96	5
β-strand	104	1	1
β-strand	111	1	2
α-helix	115-126	12
α-helix	138-141	4
α-helix	143-146	4
β-strand	149	1	3
α-helix	152-156	5
β-strand	160	1	4
α-helix	161-176	16
α-helix	182-190	9
α-helix	202-214	13
α-helix	216-218	3
α-helix	219-223	5
α-helix	225-230	6
α-helix	233-240	8
α-helix	245-252	8
α-helix	260-267	8
α-helix	273-277	5
α-helix	279-286	8
α-helix	290-303	14
β-strand	309	1	5
β-strand	312-317	6	5
β-strand	326-336	11	5
α-helix	338-340	3
β-strand	341-349	9	6
β-strand	352-359	8	6
β-strand	367-373	7	5
β-strand	376-382	7	5
α-helix	384-386	3
β-strand	387	1	6
β-strand	390-393	4	6
β-strand	396	1	6
α-helix	399-402	4
β-strand	407-413	7	5
β-strand	419-431	13	5
α-helix	434-449	16
α-helix	454-461	8
α-helix	472-487	16
α-helix	492-498	7
α-helix	502-504	3
α-helix	514-515	2
α-helix	516-520	5
β-strand	524	1	7
β-strand	527	1	7
β-strand	535-537	3	8
α-helix	540-542	3
α-helix	546-555	10
α-helix	559-569	11
β-strand	577-579	3	8
α-helix	582-597	16
α-helix	602-612	11
α-helix	614-616	3
α-helix	624-644	21
α-helix	648-655	8
α-helix	665-678	14
α-helix	688-699	12
α-helix	705-718	14
α-helix	727-737	11
α-helix	749-769	21
α-helix	773-781	9
α-helix	788-789	2
α-helix	793-795	3
α-helix	798-814	17
α-helix	815-817	3
α-helix	818-826	9
α-helix	832-839	8
α-helix	843-855	13
α-helix	871-887	17
α-helix	891-898	8
α-helix	908-911	4
α-helix	912-924	13
α-helix	928-953	26
α-helix	964-971	8
β-strand	982	1	4
α-helix	985-1001	17
α-helix	1010-1013	4
α-helix	1016-1019	4
α-helix	1021-1025	5
α-helix	1028-1039	12
α-helix	1041-1044	4
α-helix	1055-1064	10
α-helix	1071-1089	19
β-strand	1092-1098	7	9
β-strand	1107-1113	7	9
β-strand	1121-1127	7	9
β-strand	1132	1	10
β-strand	1135	1	10
α-helix	1138-1140	3
β-strand	1145-1146	2	9
α-helix	1154-1156	3
β-strand	1158-1163	6	11
β-strand	1166-1177	12	11
β-strand	1180	1	12
β-strand	1190	1	12
β-strand	1193-1202	10	11
β-strand	1203	1	13
β-strand	1209	1	13
α-helix	1210-1212	3
β-strand	1213-1216	4	11
α-helix	1218-1223	6
α-helix	1226-1227	2
α-helix	1231-1232	2
β-strand	1233-1238	6	14
β-strand	1239	1	15
β-strand	1244-1250	7	14
α-helix	1256-1259	4
β-strand	1265-1270	6	14
β-strand	1275-1277	3	14
α-helix	1278-1279	2
α-helix	1280-1289	10
β-strand	1300-1301	2	16
β-strand	1303-1304	2	9
α-helix	1305	1
β-strand	1306	1	15
α-helix	1582-1584	3
β-strand	1585-1588	4	16
β-strand	1594-1598	5	16
β-strand	1601-1604	4	16
α-helix	1609-1617	9
α-helix	1621-1624	4
α-helix	1629-1631	3
α-helix	1632	1
β-strand	1633-1635	3	17
α-helix	1636	1
β-strand	1640-1647	8	18
α-helix	1648-1650	3
α-helix	1652-1654	3
β-strand	1660-1666	7	19
β-strand	1674-1680	7	19
β-strand	1686-1693	8	18
β-strand	1705-1711	7	19
β-strand	1724-1727	4	19
β-strand	1733-1735	3	19
β-strand	1746-1749	4	18
β-strand	1755-1757	3	17
α-helix	1765-1769	5
α-helix	1770-1774	5
α-helix	1775-1785	11
α-helix	1789-1799	11
β-strand	1800	1	20
β-strand	1806-1807	2	21
β-strand	1810-1811	2	21
β-strand	1816	1	20
α-helix	1819-1823	5
α-helix	1837-1843	7
α-helix	1846-1868	23
α-helix	1873-1890	18
α-helix	1893-1895	3
β-strand	1906	1	3
α-helix	1907-1914	8
β-strand	1949	1	2
α-helix	1950	1
β-strand	1951	1	1
α-helix	1952-1953	2
α-helix	1954-1971	18
β-strand	1974	1	22
β-strand	1980	1	22
α-helix	1983-1985	3
α-helix	1989-1993	5
β-strand	2006	1	23
α-helix	2009-2012	4
β-strand	2017	1	24
α-helix	2019-2104	86
α-helix	2111-2122	12
α-helix	2125-2139	15
β-strand	2144-2146	3	25
β-strand	2148-2150	3	26
α-helix	2156-2243	88
α-helix	2248-2283	36
α-helix	2294-2296	3
β-strand	2298	1	23
α-helix	2299-2301	3
α-helix	2306-2324	19
β-strand	2329-2336	8	27
α-helix	2337-2342	6
α-helix	2354-2360	7
β-strand	2367-2368	2	28
α-helix	2371-2373	3
β-strand	2375-2377	3	28
β-strand	2387-2392	6	28
α-helix	2393-2396	4
α-helix	2398-2401	4
α-helix	2404-2406	3
β-strand	2410-2418	9	27
α-helix	2423-2424	2
β-strand	2431-2434	4	28
β-strand	2447-2450	4	28
β-strand	2456	1	27
β-strand	2468	1	24
α-helix	2469-2470	2
β-strand	2476	1	27
β-strand	2481-2486	6	28
α-helix	2491-2493	3
α-helix	2498-2501	4
β-strand	2508-2515	8	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdA1	A, B, C, D, E	protein	2535	Photorhabdus luminescens	Q9RN43

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

>8CQ0_1 TcdA1 (chains A, B, C, D, E)
MAHHHHHHSSGLEVLFQGPMNESVKEIPDVLKSQCGFNCLTDISHSSFNEFRQQVSEHLS
WSETHDLYHDAQQAQKDNRLYEARILKRANPQLQNAVHLAILAPNAELIGYNNQFSGRAS
QYVAPGTVSSMFSPAAYLTELYREARNLHASDSVYYLDTRRPDLKSMALSQQNMDIELST
LSLSNELLLESIKTESKLENYTKVMEMLSTFRPSGATPYHDAYENVREVIQLQDPGLEQL
NASPAIAGLMHQASLLGINASISPELFNILTEEITEGNAEELYKKNFGNIEPASLAMPEY
LKRYYNLSDEELSQFIGKASNFGQQEYSNNQLITPVVNSSDGTVKVYRITREYTTNAYQM
DVELFPFGGENYRLDYKFKNFYNASYLSIKLNDKRELVRTEGAPQVNIEYSANITLNTAD
ISQPFEIGLTRVLPSGSWAYAAAKFTVEEYNQYSFLLKLNKAIRLSRATELSPTILEGIV
RSVNLQLDINTDVLGKVFLTKYYMQRYAIHAETALILCNAPISQRSYDNQPSQFDRLFNT
PLLNGQYFSTGDEEIDLNSGSTGDWRKTILKRAFNIDDVSLFRLLWITDHDNKDGKIKNN
LKNLSNLYIGKLLADIHQLTIDELDLLLIAVGEGKTNLSAISDKQLATLIRKLNTITSWL
HTQKWSVFQLFIMTSTSYNKTLTPEIKNLLDTVYHGLQGFDKDKADLLHVMAPYIAATLQ
LSSENVAHSVLLWADKLQPGDGAMTAEKFWDWLNTKYTPGSSEAVETQEHIVQYCQALAQ
LEMVYHSTGINENAFRLFVTKPEMFGAATGAAPAHDALSLIMLTRFADWVNALGEKASSV
LAAFEANSLTAEQLADAMNLDANLLLQASIQAQNHQHLPPVTPENAFSCWTSINTILQWV
NVAQQLNVAPQGVSALVGLDYIQSMKETPTYAQWENAAGVLTAGLNSQQANTLHAFLDES
RSAALSTYYIRQVAKAAAAIKSRDDLYQYLLIDNQVSAAIKTTRIAEAIASIQLYVNRAL
ENVEENANSGVISRQFFIDWDKYNKRYSTWAGVSQLVYYPENYIDPTMRIGQTKMMDALL
QSVSQSQLNADTVEDAFMSYLTSFEQVANLKVISAYHDNINNDQGLTYFIGLSETDAGEY
YWRSVDHSKFNDGKFAANAWSEWHKIDCPINPYKSTIRPVIYKSRLYLLWLEQKEITKQT
GNSKDGYQTETDYRYELKLAHIRYDGTWNTPITFDVNKKISELKLEKNRAPGLYCAGYQG
EDTLLVMFYNQQDTLDSYKNASMQGLYIFADMASKDMTPEQSNVYRDNSYQQFDTNNVRR
VNNRYAEDYEIPSSVSSRKDYGWGDYYLSMVYNGDIPTINYKAASSDLKIYISPKLRIIH
NGYEGQKRNQCNLMNKYGKLGDKFIVYTSLGVNPNNSSNKLMFYPVYQYSGNTSGLNQGR
LLFHRDTTYPSKVEAWIPGAKRSLTNQNAAIGDDYATDSLNKPDDLKQYIFMTDSKGTAT
DVSGPVEINTAISPAKVQIIVKAGGKEQTFTADKDVSIQPSPSFDEMNYQFNALEIDGSG
LNFINNSASIDVTFTAFAEDGRKLGYESFSIPVTLKVSTDNALTLHHNENGAQYMQWQSY
RTRLNTLFARQLVARATTGIDTILSMETQNIQEPQLGKGFYATFVIPPYNLSTHGDERWF
KLYIKHVVDNNSHIIYSGQLTDTNINITLFIPLDDVPLNQDYHAKVYMTFKKSPSDGTWW
GPHFVRDDKGIVTINPKSILTHFESVNVLNNISSEPMDFSGANSLYFWELFYYTPMLVAQ
RLLHEQNFDEANRWLKYVWSPSGYIVHGQIQNYQWNVRPLLEDTSWNSDPLDSVDPDAVA
QHDPMHYKVSTFMRTLDLLIARGDHAYRQLERDTLNEAKMWYMQALHLLGDKPYLPLSTT
WSDPRLDRAADITTQNAHDSAIVALRQNIPTPAPLSLRSANTLTDLFLPQINEVMMNYWQ
TLAQRVYNLRHNLSIDGQPLYLPIYATPADPKALLSAAVATSQGGGWLPESFMSLWRFPH
MLENARGMVSQLTQFGSTLQNIIERQDAEALNALLQNQAAELILTNLSIQDKTIEELDAE
KTVLEKSKAGAQSRFDSYGKLYDENINAGENQAMTLRASAAGLTTAVQASRLAGAAADLV
PNIFGFAGGGSRWGAIAEATGYVMEFSANVMNTEADKISQSETYRRRRQEWEIQRNNAEA
ELKQIDAQLKSLAVRREAAVLQKTSLKTQQEQTQSQLAFLQRKFSNQALYNWLRGRLAAI
YFQFYDLAVARCLMAEQAYRWELNDDSARFIKPGAWQGTYAGLLAGETLMLSLAQMEDAH
LKRDKRALEVERTVSLAEVYAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGT
DTKTSLQASVSFADLKIREDYPASLGKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGL
ANGCEALAVSHGMNDSGQFQLDFNDGKFLPFEGIAIDQGTLTLSFPNASMPEKGKQATML
KTLNDIILHIRYTIK

Primary citation

Multistate kinetics of the syringe-like injection mechanism of Tc toxins. Ng'ang'a, P.N., Folz, J., Kucher, S. et al. Sci Adv (2025) 11:eadr2019-eadr2019. DOI 10.1126/sciadv.adr2019 · 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
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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