5LKH: Tc toxin TcdA1 in its pore state

Name: PDB 5LKH: Cryo-EM structure of the Tc toxin TcdA1 in its pore state (obtained by flexible fitting)
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 (obtained by flexible fitting). 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: 37,345
Mol. weight: 1416.15 kDa
Released: 31 Aug 2016

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

Secondary structure: helices and β-sheets

5LKH contains 205 α-helices and 180 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: 41 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	219-223	5
α-helix	225-230	6
α-helix	233-240	8
α-helix	245-252	8
α-helix	257-267	11
α-helix	273-277	5
α-helix	279-286	8
α-helix	290-296	7
β-strand	300	1	1
β-strand	306	1	1
β-strand	313-319	7	2
β-strand	324-334	11	2
β-strand	342-349	8	3
β-strand	352-358	7	3
β-strand	367-371	5	2
β-strand	377-381	5	2
α-helix	384-385	2
β-strand	390-396	7	3
α-helix	399-403	5
β-strand	406-414	9	2
β-strand	418-431	14	2
α-helix	433-450	18
α-helix	454-464	11
α-helix	472-487	16
α-helix	492-498	7
α-helix	501-503	3
α-helix	514-519	6
β-strand	536-537	2	4
α-helix	546-555	10
α-helix	559-569	11
β-strand	577-578	2	4
α-helix	582-597	16
α-helix	602-612	11
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	793-795	3
α-helix	798-814	17
α-helix	815-817	3
α-helix	818-826	9
α-helix	834-839	6
α-helix	843-855	13
α-helix	864-867	4
α-helix	871-886	16
β-strand	1319-1324	6	5
β-strand	1331	1	5
β-strand	1340-1344	5	6
β-strand	1349-1353	5	6
β-strand	1357-1359	3	7
β-strand	1360	1	5
α-helix	1367-1378	12
β-strand	1384-1392	9	8
α-helix	1393-1394	2
β-strand	1405-1410	6	8
β-strand	1420-1425	6	8
β-strand	1432-1437	6	8
β-strand	1444-1450	7	8
β-strand	1454-1458	5	8
α-helix	1466-1468	3
β-strand	1471-1475	5	8
β-strand	1480-1490	11	8
β-strand	1499-1504	6	5
β-strand	1507-1511	5	5
α-helix	1513-1516	4
β-strand	1517	1	9
α-helix	1521-1523	3
β-strand	1528-1530	3	7
β-strand	1532	1	9
β-strand	1535-1537	3	6
β-strand	1545	1	5
β-strand	1548-1558	11	5
β-strand	1564-1575	12	5

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

>5LKH_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
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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