3FIE: Botulinum neurotoxin type F

Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with an inhibitor (inh1). Determined by X-ray diffraction at 2.1 Å resolution. Released 23 Jun 2009.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Clostridium botulinum
Chains: 4
Atoms: 7,390
Mol. weight: 106.18 kDa
Ligands: ZN
Released: 23 Jun 2009

Explore 3FIE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FIE contains 38 α-helices and 49 β-strands across 4 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: 20 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-7	5
α-helix	13-14	2
β-strand	19-22	4	1
α-helix	23-24	2
β-strand	34-40	7	1
β-strand	43-49	7	1
α-helix	56-59	4
α-helix	61-62	2
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	127	1	2
β-strand	136-140	5	1
β-strand	146-150	5	1
β-strand	153-157	5	1
β-strand	166-169	4	1
β-strand	172-173	2	3
β-strand	179-180	2	3
α-helix	182-184	3
β-strand	191-194	4	1
β-strand	199-201	3	4
β-strand	202-204	3	5
β-strand	216-218	3	5
α-helix	221-236	16
α-helix	241-245	5
β-strand	247-251	5	6
β-strand	259-263	5	6
α-helix	264-270	7
α-helix	272-277	6
α-helix	280-302	23
β-strand	306	1	2
α-helix	313-323	11
β-strand	326-328	3	7
β-strand	334-336	3	7
α-helix	338-349	12
α-helix	353-359	7
β-strand	374-376	3	4
α-helix	377-378	2
β-strand	387	1	8
β-strand	391	1	8
α-helix	395-404	10
β-strand	405	1	5
α-helix	410-415	6

Chain B: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	19-22	4	9
α-helix	23-24	2
β-strand	34-40	7	9
β-strand	43-49	7	9
α-helix	56-59	4
α-helix	81-99	19
α-helix	102-113	12
α-helix	115-117	3
β-strand	127	1	10
β-strand	136-140	5	9
β-strand	146-150	5	9
β-strand	153-157	5	9
β-strand	166-169	4	9
β-strand	172-173	2	11
β-strand	179-180	2	11
α-helix	182-184	3
β-strand	191-194	4	9
β-strand	199-204	6	12
β-strand	216-218	3	12
α-helix	221-236	16
β-strand	247-251	5	13
β-strand	259-263	5	13
α-helix	264-270	7
α-helix	272-277	6
α-helix	280-303	24
β-strand	306	1	10
α-helix	313-323	11
β-strand	326-328	3	14
α-helix	329	1
β-strand	334-336	3	14
α-helix	338-349	12
α-helix	353-359	7
β-strand	373-376	4	12
β-strand	387	1	15
β-strand	391	1	15
α-helix	395-401	7
β-strand	405	1	12

Chain C: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	1
α-helix	50-53	4
β-strand	57	1	1

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	9
α-helix	37-39	3
α-helix	50-53	4
β-strand	57	1	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Botulinum neurotoxin type F	A, B	protein	427	Clostridium botulinum	A7GBG3 (AlphaFold model)
fragment of Vesicle-associated membrane protein 2	C, D	protein	38		P63027 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3FIE_1 BOTULINUM NEUROTOXIN TYPE F (chains A, B)
MPVVINSFNYNDPVNDDTILYMQIPYEEKSKKYYKAFEIMRNVWIIPERNTIGTDPSDFD
PPASLENGSSAYYDPNYLTTDAEKDRYLKTTIKLFKRINSNPAGEVLLQEISYAKPYLGN
EHTPINEFHPVTRTTSVNIKSSTNVKSSIILNLLVLGAGPDIFENSSYPVRKLMDSGGVY
DPSNDGFGSINIVTFSPEYEYTFNDISGGYNSSTESFIADPAISLAHELIHALHGLYGAR
GVTYKETIKVKQAPLMIAEKPIRLEEFLTFGGQDLNIITSAMKEKIYNNLLANYEKIATR
LSRVNSAPPEYDINEYKDYFQWKYGLDKNADGSYTVNENKFNEIYKKLYSFTEIDLANKF
KVKCRNTYFIKYGFLKVPNLLDDDIYTVSEGFNIGNLAVNNRGQNIKLNPKIIDSIPDKL
EHHHHHH

Sequence of entity 2 (C, D), FASTA

>3FIE_2 fragment of Vesicle-associated membrane protein 2 (chains C, D)
PPPNLTSNRRLQQTQAQVDEVVDIMRVNVDKVLERDCX

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Mode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F. Agarwal, R., Schmidt, J.J., Stafford, R.G. et al. Nat Struct Mol Biol (2009) 16:789-794. DOI 10.1038/nsmb.1626 · PubMed

Other PDB entries of the same protein (UniProt A7GBG3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3RSJ 2.0 Å, Structure of HCRF in complex with Ganglioside GD1a
3FUQ 2.1 Å, Glycosylated SV2 and Gangliosides as Dual Receptors for Botulinum Neurotoxin Serotype F
3FII 2.17 Å, Crystal structure of Clostridium botulinum neurotoxin serotype F catalytic domain with…

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