PDB-7t5f: Botulinum neurotoxin Type B Light Chain complexed with nanobodies...

ID or keywords:

Entry

Database: PDB / ID: 7t5f

Title

Botulinum neurotoxin Type B Light Chain complexed with nanobodies JLJ-G3 and JNE-B10

Components

Botulinum neurotoxin type B
JLJ-G3
JNE-B10

Keywords

TOXIN / Botulinum neurotoxin / camelid heavy chain antibody / endopeptidase / inhibitor

Function / homology

Function and homology information

Toxicity of botulinum toxin type B (botB) / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / host cell plasma membrane ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Camelidae (mammal)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Jin, R. / Lam, K.-H.

Funding support

United States, 1items

Citation

Journal: Plos Pathog. / Year: 2022
Title: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
Authors: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.

History

Deposition	Dec 12, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 29, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 19, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7t5f_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	7t5f_full_validation.pdf.gz	483.3 KB	Display
Data in XML	7t5f_validation.xml.gz	46.4 KB	Display
Data in CIF	7t5f_validation.cif.gz	64.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5f ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5f	HTTPS FTP

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Related structure data

Related structure data	7l6vC 7lzpC 7m1hC 7na9C C: citing same article (ref.)
Similar structure data	7t5f-2 2vdb-d 1n9w-d 5eyb-1 2qm1-2 4v2e-d 5t5w-d 4owx-d 2ejt-2 2w27-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Botulinum neurotoxin type B

D: Botulinum neurotoxin type B

C: JLJ-G3

B: JNE-B10

E: JNE-B10

F: JLJ-G3

hetero molecules

156 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Botulinum neurotoxin type B

C: JLJ-G3

B: JNE-B10

hetero molecules

defined by author
Evidence: gel filtration
78.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Botulinum neurotoxin type B

E: JNE-B10

F: JLJ-G3

hetero molecules

defined by author
Evidence: gel filtration
77.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	149.320, 88.276, 114.481
Angle α, β, γ (deg.)	90.00, 97.03, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-660- HOH

Details

Trimer confirmed by gel filtration

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Protein , 1 types, 2 molecules AD

#1: Protein	Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B Mass: 49553.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / References: UniProt: P10844, bontoxilysin

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Antibody , 2 types, 4 molecules CFBE

#2: Antibody	JLJ-G3 Mass: 13940.600 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Antibody	JNE-B10 Mass: 14104.831 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 138 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: Zn / References: bontoxilysin
#5: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / Details: 0.2 M KI, 0.1 M MES pH 6.5, 25 % PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.6→75.841 Å / Num. obs: 45137 / % possible obs: 99.2 % / Redundancy: 2.3 % / CC_1/2: 0.99 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.6→2.74 Å / Num. unique obs: 4493 / CC_1/2: 0.68

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: LcB

Resolution: 2.6→75.841 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2219	2280	5.05 %	Random selection
R_work	0.194	-	-	-
obs	0.1955	45121	98.94 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.6→75.841 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10329	0	8	130	10467

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	10547
X-RAY DIFFRACTION	f_angle_d	1.277	14234
X-RAY DIFFRACTION	f_dihedral_angle_d	13.93	3958
X-RAY DIFFRACTION	f_chiral_restr	0.057	1530
X-RAY DIFFRACTION	f_plane_restr	0.007	1853

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 (%)
2.6-2.6566	0.3171	131	0.2801	2656	X-RAY DIFFRACTION	99
2.6566-2.7184	0.2771	158	0.2583	2710	X-RAY DIFFRACTION	99
2.7184-2.7863	0.2735	158	0.2535	2642	X-RAY DIFFRACTION	100
2.7863-2.8617	0.2931	130	0.2371	2663	X-RAY DIFFRACTION	100
2.8617-2.9459	0.3114	117	0.237	2731	X-RAY DIFFRACTION	100
2.9459-3.041	0.2788	126	0.2256	2677	X-RAY DIFFRACTION	99
3.041-3.1497	0.2522	132	0.2243	2694	X-RAY DIFFRACTION	99
3.1497-3.2758	0.2484	142	0.2224	2695	X-RAY DIFFRACTION	99
3.2758-3.4249	0.2288	142	0.2072	2660	X-RAY DIFFRACTION	99
3.4249-3.6054	0.2709	144	0.1928	2685	X-RAY DIFFRACTION	99
3.6054-3.8313	0.2203	147	0.1833	2669	X-RAY DIFFRACTION	99
3.8313-4.1271	0.2097	155	0.1767	2665	X-RAY DIFFRACTION	99
4.1271-4.5424	0.164	141	0.1612	2661	X-RAY DIFFRACTION	98
4.5424-5.1996	0.1645	147	0.1556	2668	X-RAY DIFFRACTION	98
5.1996-6.5503	0.239	157	0.1918	2663	X-RAY DIFFRACTION	98
6.5503-75.841	0.1717	153	0.1682	2702	X-RAY DIFFRACTION	97

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	1.2985	0.1735	-0.22	1.7875	-0.0556	0.8836	0.0144	0.0681	0.1052	0.0934	0.0319	0.075	-0.0631	-0.0616	-0.04	0.1984	-0.0023	0.0212	0.2406	0.0194	0.1653	14.1473	-22.0204	52.4045
2	0.3978	-0.1703	0.11	2.0128	0.5673	0.5964	-0.1561	0.16	0.1796	-0.1957	0.2776	-0.7219	-0.0912	0.2574	-0.1092	0.3097	-0.055	0.0707	0.4346	0.0354	0.4196	34.9668	-13.9073	44.4775
3	2.4144	0.7191	-0.8386	1.4398	-0.8133	0.5974	0.196	0.289	-0.2432	-0.3648	-0.0043	0.0449	-0.0131	-0.0338	-0.1139	0.3906	-0.0271	0.0587	0.5056	-0.0797	0.2271	21.437	-40.0631	37.2187
4	0.8697	-0.0018	-0.1241	1.3944	0.4162	0.4553	-0.0738	0.4271	0.1682	-0.2989	0.1847	-0.1372	0.0336	0.0405	-0.0906	0.4116	-0.0555	0.06	0.4787	0.0167	0.2099	26.1359	-20.2788	37.3066
5	4.2152	1.297	0.3694	3.0879	0.9174	1.446	-0.0965	0.4818	0.8247	-0.3779	0.1282	0.1716	-0.2895	-0.1595	-0.068	0.3952	-0.0034	0.0719	0.2726	0.103	0.4668	20.9932	4.3002	44.5302
6	0.6183	0.193	0.1795	2.4967	-0.0005	0.4619	-0.0383	-0.1391	-0.2047	-0.1343	0.1058	1.2269	0.1083	-0.1519	-0.0528	0.3098	-0.003	-0.0608	0.3631	0.0951	0.7357	19.735	2.5191	4.7831
7	2.0503	0.0522	-0.3716	3.0657	0.5307	0.4596	-0.1975	0.118	0.4474	-0.4319	-0.0272	1.2025	-0.22	-0.1897	0.0815	0.1806	-0.053	-0.1453	0.2734	0.1048	1.0964	11.3347	12.7234	2.6566
8	0.7105	-0.3937	-0.3687	2.3182	0.4942	0.9695	-0.0611	-0.1777	-0.1989	0.1337	0.2314	0.2663	0.0078	0.045	-0.0891	0.2152	0.0043	0.0082	0.2596	0.0351	0.2438	33.646	-3.3858	7.6203
9	2.2259	-1.0855	-0.3512	3.1633	-0.1778	1.2735	-0.1837	-0.1584	-0.0695	0.2482	0.1248	-0.5637	0.0744	0.1969	-0.0948	0.3008	0.0322	-0.0236	0.3483	0.0012	0.3639	45.6738	1.0307	12.3826
10	2.4504	-0.5536	0.9698	1.1628	-0.9707	1.4773	-0.1663	-0.4498	0.236	0.5947	0.2396	0.2304	-0.2946	-0.3134	-0.0795	0.6293	0.1204	0.0962	0.4965	-0.0199	0.3029	29.7676	19.7629	23.0587
11	2.7918	0.2602	0.4012	2.7052	0.2685	1.8348	0.1415	-0.2304	-0.5054	0.3878	0.1054	0.487	0.0859	0.0018	-0.2647	0.3572	0.0343	0.0551	0.3145	0.0947	0.3904	30.6216	-17.3033	12.0337
12	4.4066	-0.638	-0.3317	2.1895	-1.1327	0.7364	0.0784	0.4789	-0.5802	-0.5718	0.1547	0.4345	0.4122	-0.0174	-0.1829	0.5031	-0.0902	-0.0302	0.382	-0.087	0.46	1.9442	-59.4211	47.5698
13	4.4111	-1.1237	-3.3194	8.0092	1.7347	8.5633	-0.0896	-0.1354	0.1142	-0.1813	0.2835	-0.4607	-0.2339	0.4187	-0.2027	0.4198	-0.0386	-0.0597	0.4204	-0.0413	0.3065	1.6387	-48.5978	48.5118
14	1.5435	0.3258	0.0518	1.1656	-0.2107	1.0526	-0.142	0.4306	-0.3859	-0.2587	0.2524	-0.0269	0.1143	-0.3234	-0.0892	0.3991	-0.0459	-0.0312	0.4477	-0.0206	0.3157	0.5477	-57.5806	48.0036
15	3.0429	-3.3118	-1.591	3.7198	2.3376	4.0018	0.2578	-0.2953	0.4501	0.0083	-0.0109	-0.1681	-0.4225	0.4098	-0.2316	0.609	0.0239	0.0509	0.3079	0.0184	0.3172	14.5044	-18.9232	81.92
16	0.5481	0.2213	-0.2659	1.5022	-0.2608	1.76	0.2083	-0.313	-0.0011	0.5262	-0.0716	0.335	-0.1953	-0.0222	-0.2144	0.5369	-0.059	0.1181	0.4379	0.0232	0.303	3.5602	-25.7585	78.6513
17	4.2906	3.3923	-1.6149	7.1143	-2.8803	3.8668	0.0212	-0.127	-0.3836	0.0161	-0.0129	0.2449	0.1231	-0.4818	0.0691	0.3743	-0.0726	0.1365	0.4053	0.0264	0.4634	-3.3289	-28.1228	74.2994
18	4.1189	3.2854	-1.69	7.7823	-3.4297	5.3126	0.3399	-0.5201	0.2113	0.8881	-0.4119	0.5334	-0.584	-0.1327	-0.0429	0.5209	-0.0652	0.1512	0.4391	-0.0244	0.2876	1.6634	-17.535	77.4045
19	6.1598	0.9771	-1.5719	0.2412	-0.4688	1.1047	0.1831	-0.1493	-0.3508	0.4722	0.009	0.4044	0.3395	-0.5087	-0.1584	0.7133	-0.1537	0.1901	0.5939	0.082	0.4789	-0.1965	-30.7171	84.4156
20	3.2825	-0.2606	-2.3703	1.113	0.173	4.0755	0.1373	-0.403	-0.061	0.8953	-0.2122	0.1913	0.1226	0.0749	0.135	0.6914	-0.0406	0.0128	0.4257	-0.0033	0.3883	8.531	-29.3691	80.2635
21	6.3245	3.5605	5.2437	2.6906	2.316	5.7369	0.1558	0.4731	-0.2163	-0.137	0.0192	-0.0071	0.1175	0.304	-0.0715	1.0973	-0.2913	-0.5041	0.4728	0.1003	0.8614	20.8093	1.0243	-25.7652
22	2.3543	-0.1588	1.5257	0.0122	-0.124	1.0932	0.001	-0.149	0.2036	-0.2065	-0.0913	0.2437	-0.0825	-0.2912	0.0609	1.1702	-0.1447	-0.9095	0.7325	-0.187	1.1773	5.4602	4.9537	-30.6173
23	2.7178	0.4732	-0.9759	0.647	0.1242	0.5	0.0103	0.6437	0.2275	-0.5251	-0.1326	0.5291	-0.3161	-0.2361	0.2503	0.9249	-0.1294	-0.9241	0.5605	0.2492	0.9828	16.3658	5.3774	-17.5987
24	2.1237	-0.3051	0.7231	0.6674	-0.6	1.3475	0.0503	0.3349	0.0908	-0.4628	-0.0766	0.5827	-0.2635	-0.1669	0.1416	0.6472	0.1268	-1.3235	0.4919	0.1537	1.6026	6.817	10.0625	-16.6064
25	0.823	-0.4268	1.4004	4.3329	-2.4615	4.4828	0.0339	0.0076	-0.2518	-0.3904	-0.0328	0.5528	-0.1149	-0.4555	-0.2729	1.0108	0.0778	-0.7873	0.6521	0.0752	1.3235	8.083	0.4548	-21.2805
26	6.4666	-2.9842	2.8947	1.6179	-2.1137	3.7808	-0.0077	1.0813	0.5403	-0.2041	-0.2911	0.0569	-0.1727	0.0265	0.2182	1.2368	-0.0441	-0.8021	0.6452	0.0279	1.0874	8.6827	13.1048	-28.4229
27	3.2701	0.3184	2.5652	0.1009	-0.2162	5.087	0.1579	0.3282	0.0112	-0.4946	0.1317	0.2367	-0.0842	-0.0634	-0.1451	1.2379	-0.3529	-0.5976	0.6172	0.2675	1.0537	17.0249	11.164	-22.9994
28	2.4918	2.4779	-0.3729	3.6018	-1.2253	1.9685	0.1849	-0.9772	0.9919	0.4543	-0.0924	0.6348	-0.7927	-0.3842	-0.2587	0.6649	0.28	-0.0441	0.5893	-0.0643	0.5321	3.7494	46.1249	11.1828
29	2.3142	0.461	-0.769	3.2295	0.298	1.1501	-0.1361	-0.7228	-0.1525	0.1869	0.0701	0.2505	0.0361	0.0831	0.1544	0.4227	0.1462	0.036	0.5485	0.0186	0.4952	11.454	37.6415	8.4363
30	2.5336	-0.0724	-0.2865	3.8788	-2.4283	7.3648	-0.2862	-0.3325	-0.5659	0.248	0.2183	-0.0208	-0.0003	-0.3868	0.1781	0.3843	0.0511	0.1065	0.4516	0.0384	0.4374	4.8796	35.9105	4.0959
31	4.8346	-0.4608	-0.3612	1.21	0.3872	0.322	-0.3961	-1.161	0.1721	0.3444	0.2851	-0.0302	-0.1804	-0.6837	0.1386	0.4404	0.2516	-0.0262	0.8853	0.033	0.4065	9.6234	40.146	13.1229

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 206 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 207 through 281 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 282 through 327 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 328 through 388 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 389 through 425 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 2 through 134 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 135 through 161 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 162 through 239 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 240 through 281 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 282 through 354 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 355 through 425 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 44 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 45 through 63 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 64 through 116 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 0 through 7 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 8 through 57 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 58 through 73 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 74 through 83 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 84 through 98 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 99 through 116 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 7 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 8 through 25 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 26 through 39 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 45 through 73 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 74 through 84 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 85 through 98 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 99 through 115 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 2 through 17 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 18 through 52 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 53 through 82 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 83 through 116 )

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