6RW6: Photorhabdus luminescens TcdA1

Name: PDB 6RW6: Cryo-EM structure of Photorhabdus luminescens TcdA1
Published: 2019-10-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cryo-EM structure of Photorhabdus luminescens TcdA1. Determined by electron microscopy at 2.75 Å resolution. Released 23 Oct 2019.

Method: Electron microscopy
Resolution: 2.75 Å
Organism: Photorhabdus luminescens
Chains: 5
Atoms: 98,645
Mol. weight: 1416.15 kDa
Released: 23 Oct 2019

Explore 6RW6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RW6 contains 630 α-helices and 540 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 and B: 126 helices, 108 β-strands

Element	Residues	Length	Sheet
α-helix	29-35	7
α-helix	42-69	28
α-helix	72-75	4
α-helix	78-80	3
α-helix	86-96	11
α-helix	99-101	3
β-strand	104	1	1
β-strand	111	1	2
α-helix	115-126	12
α-helix	138-141	4
β-strand	149	1	3
α-helix	152-156	5
β-strand	159-160	2	4
α-helix	161-177	17
α-helix	182-189	8
α-helix	202-214	13
α-helix	219-223	5
α-helix	225-230	6
α-helix	233-240	8
α-helix	245-252	8
α-helix	260-268	9
α-helix	273-276	4
α-helix	279-285	7
α-helix	290-296	7
β-strand	300	1	5
β-strand	306	1	5
β-strand	309	1	6
β-strand	312-318	7	6
β-strand	325-334	10	6
β-strand	341-349	9	7
β-strand	352-359	8	7
β-strand	367-372	6	6
β-strand	376-381	6	6
α-helix	385-386	2
β-strand	387	1	7
β-strand	391-396	6	7
α-helix	399-402	4
β-strand	406-413	8	6
β-strand	419-432	14	6
α-helix	433-450	18
α-helix	454-464	11
α-helix	472-488	17
α-helix	492-498	7
α-helix	501-504	4
β-strand	508	1	8
β-strand	511	1	8
α-helix	514-519	6
β-strand	524	1	9
β-strand	527	1	9
β-strand	535-537	3	10
α-helix	546-555	10
α-helix	559-569	11
β-strand	577-579	3	10
α-helix	582-596	15
α-helix	602-612	11
α-helix	624-644	21
α-helix	648-655	8
α-helix	665-677	13
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	783-786	4
α-helix	788-789	2
α-helix	792-794	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	912-923	12
α-helix	928-949	22
α-helix	950-954	5
α-helix	964-971	8
β-strand	982-983	2	4
α-helix	985-1000	16
α-helix	1010-1013	4
α-helix	1016-1019	4
α-helix	1021-1025	5
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1055-1063	9
α-helix	1071-1089	19
α-helix	1091	1
β-strand	1092-1098	7	11
β-strand	1107-1113	7	11
β-strand	1121-1127	7	11
α-helix	1128-1130	3
β-strand	1131	1	12
β-strand	1136	1	12
α-helix	1138-1140	3
β-strand	1141	1	11
β-strand	1145-1147	3	11
β-strand	1158-1163	6	13
β-strand	1166-1180	15	13
β-strand	1190-1202	13	13
β-strand	1203	1	14
β-strand	1209	1	14
α-helix	1210-1212	3
β-strand	1213-1216	4	13
α-helix	1218-1223	6
α-helix	1226-1227	2
α-helix	1231-1232	2
β-strand	1233-1239	7	15
β-strand	1244-1250	7	15
α-helix	1256-1260	5
β-strand	1265-1269	5	15
β-strand	1275-1277	3	15
α-helix	1278-1279	2
α-helix	1280-1288	9
α-helix	1291-1293	3
β-strand	1300-1301	2	16
α-helix	1302	1
β-strand	1303	1	11
α-helix	1304-1306	3
β-strand	1308	1	17
β-strand	1310-1311	2	17
β-strand	1316	1	18
β-strand	1321-1323	3	17
β-strand	1324	1	19
α-helix	1326-1328	3
β-strand	1331-1332	2	19
β-strand	1336	1	19
β-strand	1337	1	18
β-strand	1340-1345	6	20
β-strand	1348-1353	6	20
β-strand	1356-1360	5	19
α-helix	1363-1364	2
α-helix	1367-1378	12
β-strand	1384-1393	10	21
β-strand	1404-1409	6	21
α-helix	1410	1
β-strand	1421-1426	6	21
β-strand	1432-1438	7	21
β-strand	1443-1450	8	21
α-helix	1451	1
β-strand	1454-1458	5	21
α-helix	1464-1467	4
β-strand	1471-1474	4	21
β-strand	1480-1490	11	21
α-helix	1495-1497	3
β-strand	1498-1503	6	17
β-strand	1509-1512	4	17
α-helix	1513-1516	4
β-strand	1517	1	22
α-helix	1520-1523	4
β-strand	1528-1531	4	19
β-strand	1532	1	22
β-strand	1535-1538	4	20
β-strand	1545	1	17
β-strand	1548-1558	11	17
β-strand	1564-1576	13	17
α-helix	1577-1578	2
α-helix	1582-1584	3
β-strand	1585-1588	4	16
β-strand	1594-1597	4	16
β-strand	1602-1604	3	16
α-helix	1609-1616	8
α-helix	1617-1619	3
α-helix	1621-1624	4
α-helix	1629-1631	3
β-strand	1633-1635	3	23
β-strand	1640-1647	8	24
α-helix	1648-1650	3
α-helix	1652-1655	4
β-strand	1660-1666	7	25
β-strand	1673-1680	8	25
β-strand	1686-1693	8	24
β-strand	1705-1711	7	25
β-strand	1724-1727	4	25
β-strand	1733-1735	3	25
β-strand	1746-1750	5	24
β-strand	1755-1757	3	23
α-helix	1758-1759	2
α-helix	1765-1769	5
α-helix	1770-1774	5
α-helix	1775-1785	11
α-helix	1789-1796	8
β-strand	1800	1	26
β-strand	1806	1	27
β-strand	1811	1	27
β-strand	1816	1	26
α-helix	1819-1822	4
α-helix	1837-1843	7
α-helix	1846-1869	24
α-helix	1873-1890	18
α-helix	1893-1895	3
β-strand	1906	1	3
α-helix	1907-1910	4
α-helix	1913-1926	14
α-helix	1944-1946	3
α-helix	1948	1
β-strand	1949	1	2
α-helix	1950	1
β-strand	1951	1	1
α-helix	1954-1971	18
β-strand	1974	1	28
β-strand	1980	1	28
α-helix	1983-1986	4
α-helix	1988-1995	8
α-helix	2009-2012	4
β-strand	2017	1	29
α-helix	2019-2104	86
α-helix	2109-2121	13
α-helix	2125-2138	14
β-strand	2144-2146	3	30
β-strand	2148-2150	3	30
α-helix	2156-2243	88
α-helix	2248-2283	36
α-helix	2299-2301	3
α-helix	2306-2324	19
β-strand	2329-2336	8	31
α-helix	2337-2342	6
α-helix	2346-2348	3
α-helix	2353-2360	8
β-strand	2367-2368	2	32
β-strand	2375-2377	3	32
β-strand	2387-2392	6	32
α-helix	2394-2396	3
α-helix	2398-2401	4
β-strand	2410-2418	9	31
α-helix	2423-2424	2
β-strand	2431-2435	5	32
β-strand	2447-2450	4	32
β-strand	2456	1	31
β-strand	2468	1	29
α-helix	2469-2470	2
β-strand	2476	1	31
β-strand	2481-2486	6	32
α-helix	2498-2503	6
β-strand	2508-2515	8	31

Chains C, D and E: 126 helices, 108 β-strands

Element	Residues	Length	Sheet
α-helix	29-35	7
α-helix	42-69	28
α-helix	72-75	4
α-helix	78-80	3
α-helix	86-96	11
α-helix	99-101	3
β-strand	104	1	64
β-strand	111	1	65
α-helix	115-126	12
α-helix	138-141	4
β-strand	149	1	66
α-helix	152-156	5
β-strand	159-160	2	67
α-helix	161-177	17
α-helix	182-189	8
α-helix	202-214	13
α-helix	219-223	5
α-helix	225-230	6
α-helix	233-240	8
α-helix	245-252	8
α-helix	260-268	9
α-helix	273-276	4
α-helix	279-285	7
α-helix	290-296	7
β-strand	300	1	68
β-strand	306	1	68
β-strand	309	1	69
β-strand	312-318	7	69
β-strand	325-334	10	69
β-strand	341-349	9	70
β-strand	352-359	8	70
β-strand	367-372	6	69
β-strand	376-381	6	69
α-helix	385-386	2
β-strand	387	1	70
β-strand	391-395	5	70
α-helix	399-402	4
β-strand	406-413	8	69
β-strand	419-432	14	69
α-helix	433-450	18
α-helix	454-464	11
α-helix	472-488	17
α-helix	492-498	7
α-helix	501-504	4
β-strand	508	1	71
β-strand	511	1	71
α-helix	514-519	6
β-strand	524	1	72
β-strand	527	1	72
β-strand	535-537	3	73
α-helix	546-555	10
α-helix	559-569	11
β-strand	577-579	3	73
α-helix	582-596	15
α-helix	602-612	11
α-helix	624-644	21
α-helix	648-655	8
α-helix	665-677	13
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	783-786	4
α-helix	788-789	2
α-helix	792-794	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	912-923	12
α-helix	928-949	22
α-helix	950-954	5
α-helix	964-971	8
β-strand	982-983	2	67
α-helix	985-1000	16
α-helix	1010-1013	4
α-helix	1016-1019	4
α-helix	1021-1025	5
α-helix	1028-1039	12
α-helix	1041-1043	3
α-helix	1055-1063	9
α-helix	1071-1089	19
α-helix	1091	1
β-strand	1092-1098	7	74
β-strand	1107-1113	7	74
β-strand	1121-1127	7	74
α-helix	1128-1130	3
β-strand	1131	1	75
β-strand	1136	1	75
α-helix	1138-1140	3
β-strand	1141	1	74
β-strand	1145-1147	3	74
β-strand	1158-1163	6	76
β-strand	1166-1180	15	76
β-strand	1190-1202	13	76
β-strand	1203	1	77
β-strand	1209	1	77
α-helix	1210-1212	3
β-strand	1213-1216	4	76
α-helix	1218-1223	6
α-helix	1226-1227	2
α-helix	1231-1232	2
β-strand	1233-1239	7	78
β-strand	1244-1250	7	78
α-helix	1256-1260	5
β-strand	1265-1269	5	78
β-strand	1275-1277	3	78
α-helix	1278-1279	2
α-helix	1280-1288	9
α-helix	1291-1293	3
β-strand	1300-1301	2	79
α-helix	1302	1
β-strand	1303	1	74
α-helix	1304-1306	3
β-strand	1308	1	80
β-strand	1310-1311	2	80
β-strand	1316	1	81
β-strand	1321-1323	3	80
β-strand	1324	1	82
α-helix	1326-1328	3
β-strand	1331-1332	2	82
β-strand	1336	1	82
β-strand	1337	1	81
β-strand	1340-1345	6	83
β-strand	1348-1353	6	83
β-strand	1356-1360	5	82
α-helix	1363-1364	2
α-helix	1367-1378	12
β-strand	1384-1393	10	84
β-strand	1404-1409	6	84
α-helix	1410	1
β-strand	1421-1426	6	84
β-strand	1432-1438	7	84
β-strand	1443-1450	8	84
α-helix	1451	1
β-strand	1454-1458	5	84
α-helix	1464-1467	4
β-strand	1471-1474	4	84
β-strand	1480-1490	11	84
α-helix	1495-1497	3
β-strand	1498-1503	6	80
β-strand	1509-1512	4	80
α-helix	1513-1516	4
β-strand	1517	1	85
α-helix	1520-1523	4
β-strand	1528-1531	4	82
β-strand	1532	1	85
β-strand	1535-1538	4	83
β-strand	1545	1	80
β-strand	1548-1558	11	80
β-strand	1564-1576	13	80
α-helix	1577-1578	2
α-helix	1582-1584	3
β-strand	1585-1588	4	79
β-strand	1594-1597	4	79
β-strand	1602-1604	3	79
α-helix	1609-1616	8
α-helix	1617-1619	3
α-helix	1621-1624	4
α-helix	1629-1631	3
β-strand	1633-1635	3	86
β-strand	1640-1647	8	87
α-helix	1648-1650	3
α-helix	1652-1655	4
β-strand	1660-1666	7	88
β-strand	1673-1680	8	88
β-strand	1686-1693	8	87
β-strand	1705-1711	7	88
β-strand	1724-1727	4	88
β-strand	1733-1735	3	88
β-strand	1746-1750	5	87
β-strand	1755-1757	3	86
α-helix	1758-1759	2
α-helix	1765-1769	5
α-helix	1770-1774	5
α-helix	1775-1785	11
α-helix	1789-1796	8
β-strand	1800	1	89
β-strand	1806	1	90
β-strand	1811	1	90
β-strand	1816	1	89
α-helix	1819-1822	4
α-helix	1837-1843	7
α-helix	1846-1869	24
α-helix	1873-1890	18
α-helix	1893-1895	3
β-strand	1906	1	66
α-helix	1907-1910	4
α-helix	1913-1926	14
α-helix	1944-1946	3
α-helix	1948	1
β-strand	1949	1	65
α-helix	1950	1
β-strand	1951	1	64
α-helix	1954-1971	18
β-strand	1974	1	91
β-strand	1980	1	91
α-helix	1983-1986	4
α-helix	1988-1995	8
α-helix	2009-2012	4
β-strand	2017	1	92
α-helix	2019-2104	86
α-helix	2109-2121	13
α-helix	2125-2138	14
β-strand	2144-2146	3	30
β-strand	2148-2150	3	30
α-helix	2156-2243	88
α-helix	2248-2283	36
α-helix	2299-2301	3
α-helix	2306-2324	19
β-strand	2329-2336	8	93
α-helix	2337-2342	6
α-helix	2346-2348	3
α-helix	2353-2360	8
β-strand	2367-2368	2	94
β-strand	2375-2377	3	94
β-strand	2387-2392	6	94
α-helix	2394-2396	3
α-helix	2398-2401	4
β-strand	2410-2418	9	93
α-helix	2423-2424	2
β-strand	2431-2435	5	94
β-strand	2447-2450	4	94
β-strand	2456	1	93
β-strand	2468	1	92
α-helix	2469-2470	2
β-strand	2476	1	93
β-strand	2481-2486	6	94
α-helix	2498-2503	6
β-strand	2508-2515	8	93

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

>6RW6_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

Common architecture of Tc toxins from human and insect pathogenic bacteria. Leidreiter, F., Roderer, D., Meusch, D. et al. Sci Adv (2019) 5:eaax6497-eaax6497. DOI 10.1126/sciadv.aax6497 · PubMed

Other PDB entries of the same protein (UniProt Q9RN43), best resolution first:

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)
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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