4QD2: Hemagglutinin component HA33

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 25 Jun 2014.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Clostridium botulinum, Mus musculus
Chains: 10
Atoms: 19,012
Mol. weight: 274.92 kDa
Ligands: CA
Released: 25 Jun 2014

Explore 4QD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4QD2 contains 51 α-helices and 219 β-strands across 10 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: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	383-384	2	9
β-strand	389	1	10
β-strand	392-396	5	3
β-strand	406-410	5	9
β-strand	412	1	10
β-strand	416-421	6	3
β-strand	430-433	4	9
β-strand	456-459	4	9
β-strand	468-474	7	3
β-strand	480-484	5	9
α-helix	485-486	2
β-strand	494-500	7	3
α-helix	503-507	5
β-strand	510-515	6	3
β-strand	522	1	11
β-strand	525-529	5	11
α-helix	530-532	3
β-strand	536-542	7	3
β-strand	552-558	7	11
β-strand	559	1	12
β-strand	563-574	12	3
β-strand	577-588	12	3
β-strand	590	1	12
β-strand	595-599	5	11
β-strand	603-612	10	3
β-strand	617-625	9	11

Chain B: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	3
β-strand	23-28	6	4
β-strand	31-36	6	4
α-helix	41-43	3
β-strand	45-50	6	3
β-strand	55-60	6	3
β-strand	67-70	4	3
β-strand	75-79	5	3
α-helix	83-85	3
β-strand	87-93	7	3
β-strand	96-101	6	3
β-strand	105	1	5
β-strand	108	1	5
β-strand	110-113	4	3
β-strand	117	1	6
β-strand	120	1	6
α-helix	124-126	3
β-strand	127-130	4	3
α-helix	137-139	3
β-strand	141-145	5	3

Chain C: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	15-20	6	1
β-strand	27-31	5	1
β-strand	34-38	5	1
α-helix	44-46	3
β-strand	48-53	6	1
β-strand	58-63	6	1
β-strand	71-75	5	1
β-strand	82-86	5	1
α-helix	91-93	3
β-strand	95-100	6	1
β-strand	105-110	6	1
β-strand	116-121	6	1
β-strand	126-131	6	1
α-helix	136-138	3
β-strand	140-144	5	1
α-helix	145-150	6
β-strand	153-159	7	7
β-strand	165-169	5	8
β-strand	176	1	7
β-strand	177-181	5	8
α-helix	186-188	3
β-strand	190-195	6	7
β-strand	200-205	6	7
β-strand	211-215	5	7
α-helix	217-219	3
β-strand	222-227	6	7
α-helix	234-236	3
β-strand	238-242	5	7
α-helix	243	1
β-strand	249-254	6	7
β-strand	260-264	5	7
α-helix	273	1
β-strand	274	1	8
β-strand	275-279	5	7
α-helix	284-286	3
β-strand	288-291	4	7

Chain D: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	14-20	7	1
β-strand	26-31	6	1
β-strand	34-39	6	1
α-helix	44-46	3
β-strand	48-53	6	1
β-strand	58-63	6	1
β-strand	71-75	5	1
β-strand	81-86	6	1
α-helix	91-93	3
β-strand	95-100	6	1
β-strand	105-110	6	1
β-strand	117-121	5	1
β-strand	126-130	5	1
α-helix	136-138	3
β-strand	140-144	5	1
α-helix	145-150	6
β-strand	153-159	7	2
β-strand	165-171	7	2
β-strand	174-181	8	2
β-strand	189-195	7	2
β-strand	200-205	6	2
β-strand	211-215	5	2
β-strand	223-227	5	2
β-strand	238-242	5	2
β-strand	250-254	5	2
β-strand	260-264	5	2
β-strand	274-279	6	2
β-strand	288-291	4	2

Chain E: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	13
β-strand	7-10	4	14
α-helix	17	1
β-strand	19-23	5	15
β-strand	25	1	13
β-strand	35-40	6	14
β-strand	41	1	16
β-strand	45	1	16
β-strand	51-53	3	15
β-strand	59-62	4	15
β-strand	73-81	9	14
β-strand	87	1	14
β-strand	92-99	8	14
β-strand	107-108	2	17
β-strand	112-118	7	18
α-helix	121-122	2
β-strand	126-129	4	19
β-strand	132-133	2	17
β-strand	147-154	8	18
β-strand	163-165	3	19
β-strand	171-174	4	19
β-strand	186-194	9	18
α-helix	195-198	4
β-strand	202-212	11	18

Chain F: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	382-384	3	28
α-helix	388	1
β-strand	389	1	29
β-strand	392-396	5	23
β-strand	406-410	5	28
β-strand	412	1	29
β-strand	416-422	7	23
β-strand	430-433	4	28
β-strand	456-459	4	28
β-strand	468-474	7	23
β-strand	480-484	5	28
β-strand	494-500	7	23
α-helix	503-507	5
β-strand	510-515	6	23
β-strand	522-529	8	30
α-helix	530-532	3
β-strand	536-542	7	23
β-strand	552-559	8	30
β-strand	563-574	12	23
β-strand	577-588	12	23
β-strand	590	1	30
β-strand	595-599	5	30
β-strand	603-612	10	23
β-strand	617-625	9	30

Chain G: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	23
β-strand	23-28	6	24
β-strand	31-36	6	24
α-helix	41-43	3
β-strand	45-50	6	23
β-strand	55-60	6	23
β-strand	67-70	4	23
β-strand	75-79	5	23
α-helix	83-85	3
β-strand	87-93	7	23
β-strand	96-101	6	23
β-strand	105	1	25
β-strand	108	1	25
β-strand	110-113	4	23
α-helix	124	1
β-strand	125	1	24
α-helix	126	1
β-strand	127-130	4	23
α-helix	137-139	3
β-strand	141-144	4	23

Chain H: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	14-20	7	20
β-strand	27-31	5	20
β-strand	34-38	5	20
α-helix	44-46	3
β-strand	48-53	6	20
β-strand	58-63	6	20
β-strand	71-75	5	20
β-strand	82-86	5	20
α-helix	91-93	3
β-strand	95-100	6	20
β-strand	105-110	6	20
β-strand	116-121	6	20
β-strand	126-131	6	20
α-helix	136-138	3
β-strand	140-144	5	20
α-helix	145-150	6
β-strand	153-159	7	26
β-strand	165-169	5	27
β-strand	176	1	26
β-strand	177-181	5	27
β-strand	190-195	6	26
β-strand	200-205	6	26
β-strand	211-216	6	26
α-helix	217-219	3
β-strand	222-227	6	26
α-helix	234-236	3
β-strand	238-242	5	26
α-helix	243	1
β-strand	249-254	6	26
β-strand	260-264	5	26
α-helix	273	1
β-strand	274	1	27
β-strand	275-279	5	26
β-strand	287-291	5	26

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin component HA33	C, D, H, I	protein	296	Clostridium botulinum	A5HZZ6 (AlphaFold model)
Hemagglutinin component HA17	B, G	protein	147	Clostridium botulinum	A5HZZ5 (AlphaFold model)
Hemagglutinin component HA70	A, F	protein	254	Clostridium botulinum	A5HZZ4 (AlphaFold model)
Cadherin-1	E, J	protein	213	Mus musculus	P09803 (AlphaFold model)

Sequence of entity 1 (C, D, H, I), FASTA

>4QD2_1 Hemagglutinin component HA33 (chains C, D, H, I)
EHYSVIQNSLNDKIVTISCKADTNLFFYQVAGNVSLFQQTRNYLERWRLIYDSNKAAYKI
KSMDIHNTNLVLTWNAPTHNISTQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYAD
TVARNLKLSTLNNSNYIKFIIEDYIISDLNNFTCKISPILDLNKVVQQVDVTNLNVNLYT
WDYGRNQKWTIRYNEEKAAYQFFNTILSNGVLTWIFSNGNTVRVSSSNDQNNDAQYWLIN
PVSDTDETYTITNLRDTTKALDLYGGQTANGTAIQVFNYHGDDNQKWNIRNPPGSA

Sequence of entity 2 (B, G), FASTA

>4QD2_2 Hemagglutinin component HA17 (chains B, G)
GPSVERTFLPNGNYNIKSIFSGSLYLNPVSKSLTFSNESSANNQKWNVEYMAENRCFKIS
NVAEPNKYLSYDNFGFISLDSLSNRCYWFPIKIAVNTYIMLSLNKVNELDYAWDIYDTNE
NILSQPLLLLPNFDIYNSNQMFKLEKI

Sequence of entity 3 (A, F), FASTA

>4QD2_3 Hemagglutinin component HA70 (chains A, F)
GPLGSPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIY
EAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIE
NQIQFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDT
SNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLHLLNNTNSIRLLNGAIYILKVEVTE
LNNYNIRLHIDITN

Sequence of entity 4 (E, J), FASTA

>4QD2_4 Cadherin-1 (chains E, J)
DWVIPPISCPENEKGEFPKNLVQIKSNRDKETKVFYSITGQGADKPPVGVFIIERETGWL
KVTQPLDREAIAKYILYSHAVSSNGEAVEDPMEIVITVTDQNDNRPEFTQEVFEGSVAEG
AVPGTSVMKVSATDADDDVNTYNAAIAYTIVSQDPELPHKNMFTVNRDTGVISVLTSGLD
RESYPTYTLVVQAADLQGEGLSTTAKAVITVKD

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	6

Primary citation

Molecular basis for disruption of E-cadherin adhesion by botulinum neurotoxin A complex. Lee, K., Zhong, X., Gu, S. et al. Science (2014) 344:1405-1410. DOI 10.1126/science.1253823 · PubMed

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