1T3A: Neurotoxin type E

Crystal structure of Clostridium botulinum neurotoxin type E catalytic domain. Determined by X-ray diffraction at 2.16 Å resolution. Released 29 Jun 2004.

Method: X-ray diffraction
Resolution: 2.16 Å
Organism: Clostridium botulinum
Chains: 2
Atoms: 6,743
Mol. weight: 95.86 kDa
Ligands: ZN
Released: 29 Jun 2004

Explore 1T3A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1T3A contains 39 α-helices and 44 β-strands across 2 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: 19 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	11-12	2
β-strand	17-21	5	1
β-strand	29-35	7	1
β-strand	38-44	7	1
α-helix	51-54	4
β-strand	68	1	2
α-helix	76-93	18
α-helix	97-107	11
α-helix	110-112	3
β-strand	131-134	4	1
β-strand	140-143	4	1
β-strand	147-151	5	1
β-strand	155	1	2
β-strand	160-163	4	1
α-helix	167-169	3
α-helix	172-174	3
β-strand	181-184	4	1
β-strand	189-191	3	3
β-strand	192-194	3	4
β-strand	200-202	3	4
α-helix	205-220	16
β-strand	231-232	2	5
β-strand	246-247	2	5
α-helix	248-254	7
α-helix	256-261	6
α-helix	264-286	23
α-helix	293-295	3
α-helix	296-305	10
β-strand	308-310	3	6
β-strand	316-318	3	6
α-helix	320-331	12
α-helix	335-342	8
β-strand	356-359	4	3
β-strand	369	1	7
β-strand	373	1	7
α-helix	377-386	10
β-strand	387	1	4
α-helix	392-394	3
β-strand	395-396	2	3
α-helix	403-406	4

Chain B: 20 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	11-12	2
β-strand	17-21	5	8
α-helix	28	1
β-strand	29-35	7	8
β-strand	38-44	7	8
α-helix	51-54	4
α-helix	76-95	20
α-helix	97-107	11
β-strand	131-134	4	8
β-strand	140-143	4	8
β-strand	147-151	5	8
β-strand	160-163	4	8
β-strand	166	1	9
α-helix	167-169	3
β-strand	170	1	9
α-helix	172-174	3
β-strand	181-184	4	8
β-strand	189-194	6	10
β-strand	200-202	3	10
α-helix	205-220	16
β-strand	231-232	2	11
β-strand	246-247	2	11
α-helix	248-254	7
α-helix	256-261	6
α-helix	264-287	24
α-helix	293-295	3
α-helix	297-305	9
β-strand	308-310	3	12
β-strand	316-318	3	12
α-helix	320-330	11
α-helix	335-342	8
β-strand	355-358	4	10
β-strand	359	1	13
β-strand	369	1	14
β-strand	373	1	14
α-helix	377-386	10
β-strand	387	1	10
α-helix	392-394	3
β-strand	395	1	13
α-helix	396-397	2
α-helix	401-406	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
neurotoxin type E	A, B	protein	421	Clostridium botulinum	Q00496 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1T3A_1 neurotoxin type E (chains A, B)
PKINSFNYNDPVNDRTILYIKPGGCQEFYKSFNIMKNIWIIPERNVIGTTPQDFHPPTSL
KNGDSSYYDPNYLQSDEEKDRFLKIVTKIFNRINNNLSGGILLEELSKANPYLGNDNTPD
NQFHIGDASAVEIKFSNGSQDILLPNVIIMGAEPDLFETNSSNISLRNNYMPSNHGFGSI
AIVTFSPEYSFRFNDNSMNEFIQDPALTLMHELIHSLHGLYGAKGITTKYTITQKQNPLI
TNIRGTNIEEFLTFGGTDLNIITSAQSNDIYTNLLADYKKIASKLSKVQVSNPLLNPYKD
VFEAKYGLDKDASGIYSVNINKFNDIFKKLYSFTEFDLATKFQVKCRQTYIGQYKYFKLS
NLLNDSIYNISEGYNINNLKVNFRGQNANLNPRIITPITGRGLVKKIIRFCKNIVSVKGI
R

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural analysis of botulinum neurotoxin type E catalytic domain and its mutant Glu212-->Gln reveals the pivotal role of the Glu212 carboxylate in the catalytic pathway. Agarwal, R., Eswaramoorthy, S., Kumaran, D. et al. Biochemistry (2004) 43:6637-6644. DOI 10.1021/bi036278w · PubMed

Other PDB entries of the same protein (UniProt Q00496 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1T3C 1.9 Å, Clostridium botulinum type E catalytic domain E212Q mutant
1ZKW 2.17 Å, Crystal structure of Arg347Ala mutant of botulinum neurotoxin E catalytic domain
1ZL6 2.4 Å, Crystal structure of Tyr350Ala mutant of Clostridium botulinum neurotoxin E catalytic…
7K84 2.5 Å, Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5
1ZKX 2.52 Å, Crystal structure of Glu158Ala/Thr159Ala/Asn160Ala- a triple mutant of Clostridium…
7UIA 2.59 Å, Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH
1ZL5 2.6 Å, Crystal structure of Glu335Gln mutant of Clostridium botulinum neurotoxin E catalytic…
1ZN3 2.6 Å, Crystal structure of Glu335Ala mutant of Clostridium botulinum neurotoxin type E
3FFZ 2.65 Å, Domain organization in Clostridium butulinum neurotoxin type E is unique: Its…
7UIB 2.77 Å, Crystal structure of BoNT/E receptor binding domain in complex with SV2, VHH, and sialic…
7UIE 3.23 Å, Crystal structure of HcE-JLE-G6
9ARJ 3.4 Å, CryoEM structure of BoNT-NTNH-OrfX2 complex from Clostridium botulinum E1, major class

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