7RAH: Adenylate cyclase toxin RTX domain fragment

Adenylate cyclase toxin RTX domain fragment bound to M1H5 Fab and M2B10 Fab. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Bordetella pertussis
Chains: 5
Atoms: 9,183
Mol. weight: 146.49 kDa
Ligands: CA, PO4
Released: 15 Sept 2021

Explore 7RAH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RAH contains 32 α-helices and 124 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.

Chain A: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
β-strand	98	1	2
β-strand	102-106	5	2
β-strand	112	1	3
β-strand	115-119	5	4
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	4
β-strand	141	1	3
β-strand	146-151	6	5
β-strand	154-156	3	5
β-strand	160-164	5	4
α-helix	165-168	4
β-strand	174-183	10	4
α-helix	184-187	4
β-strand	192-199	8	5
β-strand	202-211	10	5

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-58	2	8
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-98	11	8
β-strand	100A-103	7	8
β-strand	107-109	3	8
β-strand	110-111	2	7
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	128-130	3
β-strand	131-132	2	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-190	5
β-strand	194-200	7	11
α-helix	201-203	3
β-strand	205-211	7	11
α-helix	212-214	3

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
β-strand	19-25	7	12
α-helix	30-32	3
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-106	5	13
β-strand	111	1	14
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-125	4
β-strand	133-139	7	15
β-strand	140	1	14
β-strand	144-147	4	16
β-strand	161-163	3	15
α-helix	164-167	4
β-strand	173-177	5	15
β-strand	195-198	4	16
β-strand	205-206	2	16

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
α-helix	7	1
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	32-39	8	18
β-strand	46-51	6	18
β-strand	57-59	3	18
α-helix	61-63	3
β-strand	64	1	17
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-97	10	18
β-strand	102-103	2	18
β-strand	107-111	5	18
β-strand	121	1	19
β-strand	136-139	4	20
β-strand	142-145	4	19
β-strand	150-153	4	21
β-strand	154	1	22
β-strand	159	1	22
β-strand	163-165	3	20
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-178	3	19
β-strand	180-184	5	20
β-strand	197-200	4	21
β-strand	205-208	4	21

Chain E: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	1057-1059	3	23
β-strand	1066-1068	3	24
β-strand	1076-1079	4	23
β-strand	1086-1088	3	24
α-helix	1093-1095	3
α-helix	1096-1102	7
β-strand	1105-1110	6	23
β-strand	1115-1117	3	23
β-strand	1127-1131	5	23
β-strand	1135-1137	3	24
β-strand	1142-1146	5	23
β-strand	1153-1155	3	24
β-strand	1162-1164	3	23
β-strand	1171-1173	3	24
β-strand	1180-1182	3	23
β-strand	1189-1191	3	24
β-strand	1200-1202	3	23
β-strand	1209-1211	3	24
α-helix	1213-1215	3
β-strand	1225	1	23
β-strand	1229-1234	6	23
β-strand	1239-1245	7	23
β-strand	1248-1255	8	23
β-strand	1259-1261	3	24
β-strand	1266-1270	5	23
β-strand	1277-1279	3	24
β-strand	1286-1288	3	23
β-strand	1295-1297	3	24
β-strand	1304-1306	3	23
β-strand	1313-1315	3	24
β-strand	1322-1324	3	23
β-strand	1342-1344	3	24
β-strand	1351-1354	4	23
β-strand	1360-1363	4	24
β-strand	1372-1375	4	23
α-helix	1379-1381	3
β-strand	1382-1387	6	24
β-strand	1390-1395	6	24
β-strand	1401-1404	4	24
α-helix	1411-1413	3
β-strand	1417-1420	4	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
M1H5 Fab Light Chain	A	protein	215	Mus musculus
M1H5 Fab Heavy Chain	B	protein	233	Mus musculus
M2B10 Fab Light Chain	C	protein	214	Mus musculus
M2B10 Fab Heavy Chain	D	protein	235	Mus musculus
Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin…	E	protein	458	Bordetella pertussis	P0DKX7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7RAH_1 M1H5 Fab Light Chain (chains A)
DIQMIQSTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPS
RFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIKRTADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (B), FASTA

>7RAH_2 M1H5 Fab Heavy Chain (chains B)
EVNLVESGGDLVKPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLEWVATISSGGTYTYY
PDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCAREIMRGGGYYFDYWSQGTTLTVS
SRSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 3 (C), FASTA

>7RAH_3 M2B10 Fab Light Chain (chains C)
IVMTQSPAILSASLGERVTMTCTASSSVSSSYLHWYQQKPGSSPKLWIYSTSNLASGVPA
RFSGSGSGTSYSLTISSMEAEDAATYYCHQYHRSPPTFGAGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (D), FASTA

>7RAH_4 M2B10 Fab Heavy Chain (chains D)
EVQLQQSGAELVRPGTSVKVSCKASGYAFTNYLIEWVKQRPGQGLEWIGVINPGIGNTNY
NEKFKGKATLTADKSSSTVYMQLSSLTSDDSAVYFCARGLNYGSSQHWYFDVWGAGTSVT
VSSRSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLEVLFQ

Sequence of entity 5 (E), FASTA

>7RAH_5 Bifunctional adenylate cyclase toxin/hemolysin CyaA,Bifunctional adenylate cyclase toxin/hemolysin CyaA (chains E)
GPGSGGAGNDSITGNAHDNFLAGGSGDDRLDGGAGNDTLVGGEGQNTVIGGAGDDVFLQD
LGVWSNQLDGGAGVDTVKYNVHQPSEERLERMGDTGIHADLQKGTVEKWPALNLFSVDHV
KNIENLHGSRLNDRIAGDDQDNELWGHDGNDTIRGRGGDDILRGGLGLDTLYGEDGNDIF
LQDDETVSDDIDGGAGLDTVDYSAMIHPGRIVAPHEYGFGIEADLSREWVRKASALGVDY
YDNVRNVENVIGTSMKDVLIGDAQANTLMGQGGDDTVRGGDGDDLLFGGDGNDMLYGDAG
NDTLYGGLGDDTLEGGAGNDWFGQTQAREHDVLRGGDGVDTYLFGVGYGHDTIYESGGGH
DTIRINAGADQLWFARQGNDLEIRILGTDDALTVHDWYRDADHRVEIIHAANQAVDQAGI
EKLVEAMAQYPDPGAAAAAPPAARVPDTLMQSLAVNWR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	19
PO4	Phosphate ion	O4 P	1

Primary citation

Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes. Goldsmith, J.A., DiVenere, A.M., Maynard, J.A. et al. PLoS Pathog (2021) 17:e1009920-e1009920. DOI 10.1371/journal.ppat.1009920 · PubMed

Other PDB entries of the same protein (UniProt P0DKX7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5CXL 1.45 Å, Crystal structure of rtx domain block V of adenylate cyclase toxin from bordetella…
9P0D 1.5 Å, Crystal structure of Sr2+-bound RTX domain block V of adenylate cyclase toxin from…
9P0C 1.7 Å, Crystal structure of Ca2+-bound RTX domain block V of adenylate cyclase toxin from…
6SUS 1.76 Å, Crystal structure of RTX domain blocks IV and V of adenylate cyclase toxin from…
9P6C 1.99 Å, RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N,…
1YRT 2.1 Å, Crystal Structure analysis of the adenylyl cyclaes catalytic domain of adenylyl cyclase…
1ZOT 2.2 Å, crystal structure analysis of the CyaA/C-Cam with PMEAPP
2COL 2.2 Å, Crystal structure analysis of CyaA/C-Cam with Pyrophosphate
1YRU 2.5 Å, Crystal Structure analysis of the adenylyl cyclaes catalytic domain of adenylyl cyclase…
7USL 2.7 Å, Integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5…
6YNU 3.12 Å, CaM-P458 complex (crystal form 1)
6YNS 3.94 Å, CaM-P458 complex (crystal form 2)

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