6L7I: TcdA1

Signal substraction of TcdB1-TccC2 and part of TcdA1. Determined by electron microscopy at 2.9 Å resolution. Released 31 Mar 2021.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Photorhabdus luminescens
Chains: 8
Atoms: 23,561
Mol. weight: 343.24 kDa
Released: 31 Mar 2021

Explore 6L7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6L7I contains 75 α-helices and 242 β-strands across 8 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.

Chain A: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2329-2336	8	1
α-helix	2337-2341	5
α-helix	2353-2362	10
β-strand	2368-2370	3	2
β-strand	2373-2377	5	2
β-strand	2387-2392	6	2
α-helix	2404-2406	3
β-strand	2410-2418	9	1
β-strand	2431-2435	5	2
β-strand	2448-2450	3	2
β-strand	2456	1	1
β-strand	2476	1	1
β-strand	2481-2486	6	2
α-helix	2498-2501	4
β-strand	2508-2515	8	1

Chain B: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2329-2336	8	3
α-helix	2337-2341	5
α-helix	2353-2362	10
β-strand	2369-2370	2	4
β-strand	2373-2374	2	4
β-strand	2375-2377	3	5
β-strand	2386-2392	7	5
α-helix	2393-2395	3
α-helix	2398-2401	4
β-strand	2410-2418	9	3
β-strand	2422-2423	2	6
β-strand	2431-2435	5	5
β-strand	2447-2450	4	5
β-strand	2456	1	3
β-strand	2476	1	3
β-strand	2481-2487	7	5
α-helix	2498-2501	4
β-strand	2508-2515	8	3

Chain C: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2329-2336	8	7
α-helix	2337-2341	5
α-helix	2353-2362	10
β-strand	2369-2370	2	8
β-strand	2373-2374	2	8
β-strand	2375-2377	3	9
β-strand	2387-2392	6	9
α-helix	2398-2400	3
β-strand	2410-2418	9	7
β-strand	2423	1	10
β-strand	2431-2435	5	9
β-strand	2448-2450	3	9
β-strand	2456	1	7
β-strand	2476	1	7
β-strand	2481-2486	6	9
β-strand	2508-2515	8	7

Chain D: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2330-2336	7	11
α-helix	2337-2342	6
α-helix	2344-2345	2
α-helix	2353-2362	10
β-strand	2375-2377	3	12
β-strand	2387-2392	6	12
α-helix	2398-2400	3
β-strand	2410-2418	9	11
β-strand	2431-2435	5	12
β-strand	2449-2450	2	12
β-strand	2456	1	11
β-strand	2476	1	11
β-strand	2481-2486	6	12
α-helix	2498-2501	4
β-strand	2508-2515	8	11

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2329-2336	8	13
α-helix	2337-2342	6
α-helix	2353-2363	11
β-strand	2369-2370	2	14
β-strand	2373-2374	2	14
β-strand	2375-2377	3	15
β-strand	2386-2392	7	15
α-helix	2398-2400	3
α-helix	2404-2406	3
β-strand	2410-2418	9	13
β-strand	2431-2433	3	15
β-strand	2448-2450	3	15
β-strand	2456	1	13
β-strand	2476	1	13
β-strand	2481-2487	7	15
α-helix	2498-2502	5
β-strand	2508-2515	8	13

Chain F: 43 helices, 124 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
β-strand	27-28	2	16
α-helix	29-31	3
β-strand	38-42	5	16
β-strand	56-60	5	16
β-strand	61	1	17
β-strand	63	1	17
β-strand	65-67	3	18
β-strand	69-70	2	18
β-strand	72-73	2	16
β-strand	78-81	4	19
β-strand	96-97	2	19
α-helix	102	1
β-strand	103	1	19
β-strand	104-106	3	20
α-helix	107	1
β-strand	108	1	21
β-strand	114	1	21
β-strand	116-122	7	20
β-strand	125-138	14	20
β-strand	140	1	20
β-strand	146-150	5	20
β-strand	152	1	20
β-strand	155	1	22
β-strand	157	1	22
β-strand	160-164	5	20
β-strand	167	1	20
β-strand	170-173	4	20
α-helix	177-179	3
β-strand	180-182	3	19
β-strand	190-194	5	19
β-strand	195-199	5	20
β-strand	205-212	8	20
α-helix	220-225	6
β-strand	233-242	10	20
β-strand	262-269	8	20
α-helix	289-291	3
β-strand	298	1	23
β-strand	305	1	23
β-strand	313-318	6	20
α-helix	320-323	4
α-helix	332-333	2
β-strand	334-345	12	20
β-strand	350-361	12	20
β-strand	365-368	4	20
α-helix	369-371	3
β-strand	372-376	5	20
β-strand	386-390	5	24
β-strand	402-405	4	25
β-strand	414-418	5	25
β-strand	423-426	4	25
β-strand	428-430	3	26
β-strand	439-441	3	26
β-strand	445-446	2	25
β-strand	450	1	10
β-strand	457-460	4	27
β-strand	469-473	5	27
β-strand	478-482	5	27
β-strand	483	1	28
α-helix	488	1
β-strand	489	1	28
α-helix	490	1
β-strand	493-494	2	27
β-strand	498-499	2	6
α-helix	500-503	4
β-strand	508-510	3	29
β-strand	519-523	5	29
β-strand	527-531	5	29
β-strand	533	1	30
β-strand	538	1	30
β-strand	544-545	2	29
α-helix	546-547	2
β-strand	562-566	5	31
β-strand	575-579	5	31
β-strand	584-587	4	31
α-helix	588	1
β-strand	589-591	3	32
β-strand	594-595	2	32
β-strand	599-601	3	31
α-helix	613-615	3
β-strand	616-619	4	33
α-helix	627	1
β-strand	628-632	5	33
β-strand	637-640	4	33
β-strand	642	1	34
β-strand	648	1	34
β-strand	652-653	2	33
α-helix	655-657	3
β-strand	667-671	5	24
β-strand	680-685	6	24
β-strand	691-696	6	24
α-helix	701	1
β-strand	705-709	5	20
β-strand	714-722	9	20
α-helix	723-734	12
β-strand	744	1	20
β-strand	750-759	10	20
β-strand	765-778	14	20
β-strand	783-797	15	20
α-helix	807-809	3
β-strand	810-817	8	20
α-helix	821-824	4
α-helix	827-829	3
α-helix	838-842	5
β-strand	845-850	6	20
β-strand	853-856	4	20
α-helix	865-870	6
β-strand	875-883	9	20
β-strand	895-907	13	20
α-helix	913-914	2
β-strand	915-927	13	20
β-strand	938-945	8	20
β-strand	951-958	8	20
α-helix	959-963	5
α-helix	976-978	3
β-strand	989-1004	16	20
β-strand	1007-1024	18	20
α-helix	1029	1
α-helix	1035-1038	4
β-strand	1052-1062	11	20
α-helix	1069	1
β-strand	1070	1	20
β-strand	1078-1088	11	20
α-helix	1091-1094	4
α-helix	1104-1110	7
β-strand	1113-1116	4	20
β-strand	1128-1133	6	20
β-strand	1135-1138	4	35
β-strand	1147-1151	5	35
β-strand	1159-1160	2	35
β-strand	1163	1	36
β-strand	1170	1	36
β-strand	1173-1174	2	35
β-strand	1180-1181	2	35
β-strand	1182-1186	5	37
β-strand	1191-1196	6	37
β-strand	1202-1207	6	37
β-strand	1213-1221	9	37
β-strand	1226-1228	3	37
α-helix	1230-1231	2
α-helix	1243-1247	5
β-strand	1257-1262	6	37
α-helix	1263-1266	4
α-helix	1272-1275	4
α-helix	1280-1287	8
β-strand	1292	1	38
β-strand	1298	1	38
α-helix	1300-1309	10
α-helix	1315-1321	7
β-strand	1329-1335	7	37
β-strand	1346-1353	8	37
β-strand	1359-1366	8	37
β-strand	1369-1371	3	39
β-strand	1372	1	37
β-strand	1373-1374	2	39
β-strand	1380-1387	8	39
β-strand	1390-1394	5	37
β-strand	1397-1399	3	40
β-strand	1405-1409	5	40
α-helix	1410-1411	2
β-strand	1412-1414	3	37
α-helix	1419-1421	3
α-helix	1422-1427	6
β-strand	1431-1436	6	40
β-strand	1442-1446	5	40
β-strand	1452-1457	6	40
β-strand	1461-1465	5	40

Chain G: 8 helices, 58 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	14-18	5	40
β-strand	24-31	8	40
β-strand	40-48	9	40
β-strand	54-58	5	40
α-helix	60-64	5
β-strand	71-72	2	40
β-strand	73-75	3	41
β-strand	81-86	6	41
β-strand	90-96	7	41
β-strand	102-106	5	41
β-strand	112-117	6	41
β-strand	126-132	7	41
β-strand	138-145	8	41
α-helix	150-154	5
β-strand	161-166	6	41
β-strand	169-176	8	41
β-strand	182-189	8	41
β-strand	190	1	42
β-strand	210	1	42
β-strand	215-221	7	41
β-strand	227-231	5	41
β-strand	237-242	6	41
β-strand	248-254	7	41
β-strand	261-269	9	41
β-strand	275-280	6	41
α-helix	284	1
β-strand	285-290	6	41
β-strand	297-304	8	41
β-strand	309-318	10	41
β-strand	324-329	6	41
α-helix	343-345	3
β-strand	346-347	2	41
β-strand	348-350	3	43
β-strand	356-364	9	43
α-helix	374-377	4
β-strand	378	1	44
β-strand	386-395	10	43
β-strand	401-408	8	43
β-strand	413-418	6	43
β-strand	419-421	3	45
β-strand	428-430	3	45
α-helix	441-443	3
β-strand	444	1	46
β-strand	450	1	46
β-strand	454	1	47
β-strand	457	1	47
β-strand	458-461	4	44
β-strand	467-471	5	44
β-strand	477-481	5	44
β-strand	487-494	8	44
β-strand	501-508	8	44
β-strand	511-517	7	44
β-strand	522-531	10	44
β-strand	539-546	8	44
α-helix	553	1
β-strand	556-562	7	44
β-strand	568-572	5	44
β-strand	578-584	7	44
β-strand	590-595	6	44
β-strand	606-608	3	48
β-strand	611-613	3	48
β-strand	619-621	3	48
β-strand	624-627	4	48
β-strand	632-633	2	48
β-strand	659-660	2	49

Chain H: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	666-667	2	49
α-helix	670-672	3
α-helix	674-675	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TcdA1	A, B, C, D, E	protein	190	Photorhabdus luminescens	Q9RN43
TcdB1	F	protein	1476	Photorhabdus luminescens	Q93EP6
TccC2	G	protein	664	Photorhabdus luminescens	Q93EP1 (AlphaFold model)
TccC2	H	protein	16	Photorhabdus luminescens	Q93EP1 (AlphaFold model)

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

>6L7I_1 TcdA1 (chains A, B, C, D, E)
RALEVERTVSLAEVYAGLPKDNGPFSLAQEIDKLVSQGSGSAGSGNNNLAFGAGTDTKTS
LQASVSFADLKIREDYPASLGKIRRIKQISVTLPALLGPYQDVQAILSYGDKAGLANGCE
ALAVSHGMNDSGQFQLDFNDGKFLPFEGIAIDQGTLTLSFPNASMPEKGKQATMLKTLND
IILHIRYTIK

Sequence of entity 2 (F), FASTA

>6L7I_2 TcdB1 (chains F)
MQNSQTFSVTELSLPKGGGAITGMGEALTPAGPDGMAALSLPLPISAGRGYAPSLTLNYN
SGTGNSPFGLGWDCGVMAIRRRTSTGVPNYDETDTFLGPEGEVLVVALNEAGQADIRSES
SLQGINLGATFTVTCYRSRLESHFNRLEYWQPQTTGATDFWLIYSPDGQVHLLGKNPQAR
ISNPLNVNQTAQWLLEASISSHSEQIYYQYRAEDEAGCETDELAAHPSATVQRYLQTVHY
GNLTASDVFPTLNGDDPLKSGWMFCLVFDYGERKNSLSEMPLFKATGNWLCRKDRFSRYE
YGFELRTRRLCRQILMFHRLQTLSGQAKGDDEPALVSRLILDYDENAMVSTLVSVRRVGH
EDNNTVTALPPLELAYQPFEPEQTALWQSMDVLANFNTIQRWQLLDLKGEGVPGILYQDR
NGWWYRSAQRQAGEEMNAVTWGKMQLLPITPAVQDNASLMDINGDGQLDWVITGPGLRGY
HSQHPDGSWTRFTPLHALPIEYSHPRAQLADLMGAGLSDLVLIGPKSVRLYVNNRDGFTE
GRDVVQSGDITLPLPGADARKLVAFSDVLGSGQAHLVEVSATQVTCWPNLGHGRFGQPIV
LPGFSQSAASFNPDRVHLADLDGSGPADLIYVHADRLDIFSNESGNGFAKPFTLSFPDGL
RFDDTCQLQVADVQGLGVVSLILSVPHMAPHHWRCDLTNAKPWLLSETNNNMGANHTLHY
RSSVQFWLDEKAAALATGQTPVCYLPFPVHTLWQTETEDEISGNKLVTTLRYAHGAWDGR
EREFRGFGYVEQTDSHQLAQGNAPERTPPALTKSWYATGLPAVDNALSAGYWRGDKQAFA
GFTPRFTLWKEGKDVPLTPEDDHNLYWLNRALKGQPLRSELYGLDGSAQQQIPYTVTESR
PQVRQLQDGATVSPVLWASVVESRSYHYERIISDPQCNQDITLSSDLFGQPLKQVSVQYP
RRNKPTTNPYPDTLPDTLFASSYDDQQQLLRLTCRQSSWHHLIGNELRVLGLPDGTRSDA
FTYDAKQVPVDGLNLETLCAENSLIADDKPREYLNQQRTFYTDGKNQTPLKTPTRQALIA
FTETAVLTESLLSAFDGGITPDELPGILTQAGYQQEPYLFPRTGENKVWVARQGYTDYGT
EAQFWRPVAQRNSLLTGKMTLKWDTHYCVITQTQDAAGLTVSANYDWRFLTPTQLTDIND
NVHLITLDALGRPVTQRFWGIESGVATGYSSSEEKPFSPPNDIDTAINLTGPLPVAQCLV
YAPDSWMPLFSQETFNTLTQEEQETLRDSRIITEDWRICALTRRRWLQSQKISTPLVKLL
TNSIGLPPHNLTLTTDRYDRDSEQQIRQQVAFSDGFGRLLQASVRHEAGEAWQRNQDGSL
VTKVENTKTRWAVTGRTEYDNKGQTIRTYQPYFLNDWRYVSDDSARKEAYADTHIYDPIG
REIRVITAKGWLRQSQYFPWFTVSEDENDTAADALV

Sequence of entity 3 (G), FASTA

>6L7I_3 TccC2 (chains G)
MSSYNSAIDQKTPSIKVLDNRKLNVRTLEYLRTQADENSDELITFYEFNIPGFQVKSTDP
RKNKNQSGPNFIRVFNLAGQVLREESVDAGRTITLNDIESRPVLIINATGVRQNHRYEDN
TLPGRLLAITEQVQAGEKTTERLIWAGNTPQEKDYNLAGQCVRHYDTAGLTQLNSLSLAG
VVLSQSQQLLVDDKNADWTGEDQSLWQQKLSSDVYTTQNKADATGALLTQTDAKGNIQRL
AYDVAGQLKGCWLTLKGQAEQVIIKSLTYSAAGQKLREEHGNGVITEYSYEPETQRLIGI
ATRRPSDAKVLQDLRYQYDPVGNVINIRNDAEATRFWRNQKVVPENSYTYDSLYQLISAT
GREMANIGQQNNQLPSPALPSDNNTYTNYTRSYSYDHSGNLTQIRHSSPATQNNYTVAIT
LSNRSNRGVLSTLTTDPNQVDTLFDAGGHQTSLLPGQTLIWTPRGELKQVNNGPGNEWYR
YDSNGMRQLKVSEQPTQNTTQQQRVIYLPGLELRTTQSNATTTEELHVITLGEAGRAQVR
VLHWESGKPEDVNNNQLRYSYDNLIGSSQLELDNQGQIISEEEYYPFGGTALWAANSQTE
ASYKTIRYSGKERDATGLYYYGYRYYQPWAGRWLSADPAGTIDGLNLYRMVRNNPVSLQD
ENGL

Sequence of entity 4 (H), FASTA

>6L7I_4 TccC2 (chains H)
APEKGKYTKEVNFFDE

Primary citation

Signal substraction of TcdB1-TccC2 and part of TcdA1. Yan, Z.F., Zhang, N., Yang, G.W. To be published.

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

6RW6 2.75 Å, Cryo-EM structure of Photorhabdus luminescens 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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