PDB-3v0a: 2.7 angstrom crystal structure of BoNT/Ai in complex with NTNHA

ID or keywords:

Entry

Database: PDB / ID: 3v0a

Title

2.7 angstrom crystal structure of BoNT/Ai in complex with NTNHA

Components

BoNT/A
Llama antibody F12
NTNH

Keywords

TOXIN / Botulinum neurotoxin / Neurotoxin associated protein / Progenitor toxin complex / VHH bound interlocked complex / NTNHA

Function / homology

Function and homology information

bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity /

metalloendopeptidase activity /

toxin activity / host cell plasma membrane /

proteolysis / zinc ion binding ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.703 Å

Authors

Gu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.

Citation

Journal: Science / Year: 2012
Title: Botulinum neurotoxin is shielded by NTNHA in an interlocked complex.
Authors: Gu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.

History

Deposition	Dec 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 14, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3v0a.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb3v0a.ent.gz	895.4 KB	Display	PDB format
PDBx/mmJSON format	3v0a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v0/3v0a ftp://data.pdbj.org/pub/pdb/validation_reports/v0/3v0a	HTTPS FTP

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Related structure data

Related structure data	3v0bC 3v0cC C: citing same article (ref.)
Similar structure data	6rgl-d 4266 6koq-d 3ecs-d 2o5j-2 4xtk-d 1de4-2 6xjd-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: BoNT/A

B: NTNH

C: Llama antibody F12

hetero molecules

307 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	156.080, 156.080, 324.603
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 2 types, 2 molecules AB

#1: Protein	BoNT/A / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT Mass: 149449.828 Da / Num. of mol.: 1 / Mutation: E224Q,R363A,Y366F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/a, boNT/A, bonta / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS
#2: Protein	NTNH / Type A progenitor toxin nontoxic-nonHA Mass: 138450.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ant, ntnh / Production host: Escherichia coli (E. coli) / References: UniProt: Q45914

#1: Protein

BoNT/A / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT

Mass: 149449.828 Da / Num. of mol.: 1 / Mutation: E224Q,R363A,Y366F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium botulinum (bacteria) / Gene: bont/a, boNT/A, bonta / Production host:

Escherichia coli (E. coli) / References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS

#2: Protein

NTNH / Type A progenitor toxin nontoxic-nonHA

Mass: 138450.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Clostridium botulinum (bacteria) / Gene: ant, ntnh / Production host:

Escherichia coli (E. coli) / References: UniProt: Q45914

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Antibody , 1 types, 1 molecules C

#3: Antibody	Llama antibody F12 Mass: 16163.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 320 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#7: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer) Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 12% PEG MME2000, 16% pentaerythritol propoxylate(5/4 PO/OH), 0.1 M ammonium sulfate and 50mM MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.7→49.8 Å / Num. all: 109722 / Num. obs: 109570 / % possible obs: 99.9 % / Observed criterion σ(F): 13.6 / Observed criterion σ(I): 13.6 / Redundancy: 6.2 % / R_merge(I) obs: 0.127
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 6.1 % / R_merge(I) obs: 0.768 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.2_869)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.703→49.357 Å / SU ML: 0.79 / Isotropic thermal model: RANDOM / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2239	5474	5 %	RANDOM
R_work	0.1759	-	-	-
all	0.1783	109722	-	-
obs	0.1783	109570	99.59 %	-

Solvent computation

Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.598 Å² / k_sol: 0.324 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	7.0759 Å²	0 Å²	-0 Å²
2-	-	7.0759 Å²	-0 Å²
3-	-	-	-14.1518 Å²

Refinement step

Cycle: LAST / Resolution: 2.703→49.357 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20719	0	150	294	21163

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	21300
X-RAY DIFFRACTION	f_angle_d	1.017	28873
X-RAY DIFFRACTION	f_dihedral_angle_d	15.34	7867
X-RAY DIFFRACTION	f_chiral_restr	0.076	3150
X-RAY DIFFRACTION	f_plane_restr	0.004	3704

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.7034-2.7342	0.3144	151	0.2899	3264	X-RAY DIFFRACTION	95
2.7342-2.7663	0.3488	182	0.2839	3424	X-RAY DIFFRACTION	100
2.7663-2.8001	0.3516	172	0.2789	3441	X-RAY DIFFRACTION	99
2.8001-2.8355	0.3241	193	0.2628	3430	X-RAY DIFFRACTION	100
2.8355-2.8728	0.3332	180	0.265	3378	X-RAY DIFFRACTION	100
2.8728-2.9122	0.3063	188	0.2586	3426	X-RAY DIFFRACTION	100
2.9122-2.9538	0.3176	191	0.2583	3421	X-RAY DIFFRACTION	100
2.9538-2.9978	0.327	199	0.2449	3427	X-RAY DIFFRACTION	100
2.9978-3.0447	0.2928	176	0.2271	3419	X-RAY DIFFRACTION	100
3.0447-3.0946	0.2681	185	0.2321	3435	X-RAY DIFFRACTION	100
3.0946-3.1479	0.2952	183	0.2276	3429	X-RAY DIFFRACTION	100
3.1479-3.2052	0.2699	179	0.2215	3448	X-RAY DIFFRACTION	100
3.2052-3.2668	0.251	199	0.2103	3442	X-RAY DIFFRACTION	100
3.2668-3.3335	0.3016	186	0.2064	3440	X-RAY DIFFRACTION	100
3.3335-3.4059	0.2536	187	0.2022	3445	X-RAY DIFFRACTION	100
3.4059-3.4851	0.2462	188	0.1924	3445	X-RAY DIFFRACTION	100
3.4851-3.5723	0.2468	189	0.1829	3452	X-RAY DIFFRACTION	100
3.5723-3.6688	0.2249	166	0.1769	3482	X-RAY DIFFRACTION	100
3.6688-3.7768	0.2093	193	0.1655	3465	X-RAY DIFFRACTION	100
3.7768-3.8986	0.1977	175	0.1533	3469	X-RAY DIFFRACTION	100
3.8986-4.0379	0.193	181	0.1403	3468	X-RAY DIFFRACTION	100
4.0379-4.1995	0.1834	177	0.1291	3498	X-RAY DIFFRACTION	100
4.1995-4.3905	0.1727	180	0.125	3503	X-RAY DIFFRACTION	100
4.3905-4.6218	0.1456	186	0.117	3508	X-RAY DIFFRACTION	100
4.6218-4.9111	0.1564	179	0.1193	3525	X-RAY DIFFRACTION	100
4.9111-5.2899	0.1882	183	0.135	3509	X-RAY DIFFRACTION	100
5.2899-5.8215	0.1927	157	0.1644	3584	X-RAY DIFFRACTION	100
5.8215-6.6622	0.2324	178	0.1818	3552	X-RAY DIFFRACTION	100
6.6622-8.3869	0.1939	188	0.1549	3628	X-RAY DIFFRACTION	100
8.3869-49.365	0.1918	203	0.1701	3739	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.9512	1.4961	0.0849	2.8822	-0.4817	1.3067	-0.1629	0.3073	0.1921	-0.476	0.0125	-0.2574	-0.1845	0.5464	0.1172	0.3766	-0.2022	0.0433	0.664	0.0271	0.3043	110.5507	85.689	7.2829
2	0.9971	0.1742	0.2563	1.2053	-0.2029	1.0782	-0.0214	0.0016	0.2039	0.1393	-0.0387	-0.1403	-0.233	0.3561	0.0428	0.2611	-0.1698	0.0356	0.5247	-0.0612	0.2437	109.0065	81.8933	24.7236
3	0.8924	0.5299	0.7818	0.7191	0.0258	2.1076	0.1999	-0.1099	-0.0645	0.0262	-0.0779	-0.2559	-0.1332	0.3318	0.0003	0.2159	-0.0856	0.0082	0.5681	-0.0663	0.2499	112.2602	59.5294	29.6051
4	0.4812	0.1863	0.3768	1.2531	0.049	0.7336	0.0782	0.0122	0.0263	0.0086	-0.0167	-0.1087	0.0521	0.2242	-0.0622	0.2119	-0.0036	0.0569	0.4891	-0.0258	0.2121	100.5755	55.367	18.8927
5	0.2514	0.3762	1.0496	0.7637	1.22	3.3282	0.0234	0.0294	0.0117	0.075	0.0805	-0.04	0.0464	0.3455	-0.1154	0.1795	-0.0313	0.023	0.377	-0.028	0.1906	99.853	54.7675	37.4286
6	0.3274	0.2575	0.3806	0.4054	0.1389	1.0604	-0.04	-0.0346	0.0801	-0.0079	0.0635	0.1699	-0.0676	-0.2004	-0.0215	0.1678	0.013	0.0456	0.3953	0.0588	0.2711	60.4862	65.741	31.2473
7	3.4819	1.0347	3.1108	2.8727	-1.7423	6.3719	0.268	-0.0952	0.1032	0.168	-0.2311	0.3012	0.2982	-0.3378	-0.0761	0.3381	0.0956	0.1473	0.4563	-0.042	0.3025	49.6489	69.1267	54.3207
8	2.3499	0.1414	-1.0886	0.7061	-0.0215	1.932	0.1	0.2154	-0.0021	0.0712	0.0498	0.1485	-0.0263	-0.3379	-0.1352	0.2677	-0.0592	0.021	0.1615	0.0705	0.1616	43.8283	29.9779	57.9552
9	0.7545	0.1775	0.3657	1.2112	0.0935	1.0005	-0.0017	0.053	-0.0422	-0.0193	0.0507	0.0861	0.0678	-0.0933	-0.0279	0.0722	0.004	0.0907	0.2557	0.04	0.0719	64.732	42.0892	42.9586
10	1.4704	-0.4382	-0.2346	2.9572	-1.3419	2.0655	0.1081	-0.0977	0.4443	0.2431	0.0714	-0.0894	-0.5326	-0.0615	-0.109	0.289	-0.0385	0.0385	0.2733	-0.0808	0.2643	81.7459	79.2819	52.0714
11	3.4614	0.8307	0.721	2.5378	-1.2823	1.0563	0.6705	-0.081	1.26	-0.0963	-0.3288	-0.2365	-1.6622	0.6041	-0.3504	1.2109	-0.5854	0.2416	0.9966	0.3747	1.3841	123.1994	114.3455	-9.2465
12	3.7567	-2.3058	0.091	2.8063	-1.8498	2.3129	0.377	1.3682	0.387	-0.6255	-0.7225	-0.0145	0.4782	-0.0006	0.2734	1.0203	-0.1895	0.2971	1.5943	-0.0955	1.2732	127.1676	98.1285	-28.3743
13	2.6754	-0.1009	-0.1261	0.6763	1.5937	5.8649	0.34	-0.0349	0.5817	-0.4545	-0.3403	-0.6351	-0.8533	0.9549	-0.166	1.057	-0.6254	0.2244	1.1345	0.1413	0.8508	127.9415	106.5982	-7.6077
14	4.6137	-1.1719	-2.3666	2.5944	-0.4706	8.7869	0.3345	0.8795	-0.019	-0.7526	-0.553	0.0102	-0.0778	-0.7323	0.2458	1.188	-0.2297	-0.0723	1.3596	0.0551	0.6559	116.4608	100.2188	-15.4438
15	6.1327	3.2448	3.3459	3.5902	1.0458	2.3699	-0.5226	0.715	-0.132	-0.5508	0.0669	0.0135	0.4385	-0.456	0.4016	0.577	-0.4053	0.18	1.6187	0.0827	0.619	123.4584	95.9437	-5.9815
16	2.7239	-0.5278	1.526	1.9718	0.0408	0.9155	-0.0322	0.6951	-0.3987	-1.0017	0.0051	-0.6335	-0.3704	1.2758	0.0537	1.0678	-0.2153	0.3103	1.3577	-0.1456	1.1647	124.2706	89.6305	-14.4307
17	3.6072	1.7616	-0.6376	3.0153	-1.5103	0.7803	0.033	0.198	0.1342	-0.1395	-0.3504	-0.8523	-0.6264	0.8081	0.2801	0.8971	-0.5524	0.2335	1.5822	0.1118	0.9018	133.8699	104.3682	-6.824
18	3.238	0.5857	-0.0152	2.6812	-1.7447	1.1784	-0.0974	0.8103	-0.0436	-0.4883	-0.0466	-0.817	-0.1514	0.903	0.1753	1.0783	-0.5381	0.4775	1.574	-0.04	0.8843	130.6044	100.5018	-14.2257
19	0.336	-0.1829	-0.817	0.4505	0.5162	2.246	0.0566	0.5848	-0.2266	-1.1709	-0.3329	-0.6871	-0.517	0.7709	0.1891	1.2369	-0.3007	0.1396	1.6952	0.096	0.6997	120.0965	97.9899	-15.8908
20	2.1524	0.5695	-1.0171	3.1843	1.2774	5.7369	0.8381	0.538	-0.0236	-0.9281	-0.3197	0.1916	-0.6519	0.4757	-0.5493	1.3102	-0.2632	-0.1677	1.3889	0.2103	0.5978	116.3865	105.4665	-13.7236

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 1:99)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 100:412)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 413:495)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 496:628)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 629:825)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 826:1194)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 1195:1295)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 1:536)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 537:910)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 911:1194)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 0:7)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 8:16)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 17:33)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 34:44)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 45:59)
16	X-RAY DIFFRACTION	16	chain 'C' and (resseq 60:67)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 68:76)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 77:83)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 84:101)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 102:118)

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Protein , 2 types, 2 molecules AB

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Antibody , 1 types, 1 molecules C

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Non-polymers , 5 types, 320 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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-Components

-Protein , 2 types, 2 molecules AB

-Antibody , 1 types, 1 molecules C

-Non-polymers , 5 types, 320 molecules

-Experimental details

-Experiment

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-Data collection

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+About Yorodumi

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Protein , 2 types, 2 molecules AB

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Non-polymers , 5 types, 320 molecules

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