PDB-7k84: Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5

ID or keywords:

Entry

Database: PDB / ID: 7k84

Title

Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5

Components

Botulinum neurotoxin type E
JLE-E5

Keywords

ANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN

Function / homology

Function and homology information

Toxicity of botulinum toxin type E (botE) / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Vicugna pacos (alpaca)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Lam, K. / Jin, R.

Funding support

United States, 4items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI139087	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R21AI139690	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R21AI123920	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI125704	United States

Citation

Journal: Toxins / Year: 2020
Title: Two VHH Antibodies Neutralize Botulinum Neurotoxin E1 by Blocking Its Membrane Translocation in Host Cells.
Authors: Lam, K.H. / Perry, K. / Shoemaker, C.B. / Jin, R.

History

Deposition	Sep 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7k84.cif.gz	425.8 KB	Display	PDBx/mmCIF format
PDB format	pdb7k84.ent.gz	309.2 KB	Display	PDB format
PDBx/mmJSON format	7k84.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7k84_validation.pdf.gz	448.6 KB	Display	wwPDB validaton report
Full document	7k84_full_validation.pdf.gz	458.8 KB	Display
Data in XML	7k84_validation.xml.gz	33 KB	Display
Data in CIF	7k84_validation.cif.gz	44.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k8/7k84 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/7k84	HTTPS FTP

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Related structure data

Related structure data	7k7yC 3ffzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2xqy-2 7l0r-d 7e2z-d 5dgk-d 1te0-d 6ni3-d 4wc7-d 6gdg-d 3wfq-4 7d76-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	#167 - Nov 2013 SNARE Proteins similarity (1)

Deposited unit

A: Botulinum neurotoxin type E

B: JLE-E5

hetero molecules

111 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	96.086, 49.877, 133.508
Angle α, β, γ (deg.)	90.000, 101.037, 90.000
Int Tables number	3
Space group name H-M	P121
Space group name Hall	P2y
Symmetry operation	#1: x,y,z #2: -x,y,-z

#1: Protein	Botulinum neurotoxin type E Mass: 96816.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont, FDB75_10755 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6B4PXW0, UniProt: Q00496*PLUS
#2: Protein	JLE-E5 Mass: 13981.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.15 M Ammonium sulfate, 14% PEG 4000, 0.1 M Hepes (pH 7.0)

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.5→131.04 Å / Num. obs: 43226 / % possible obs: 96.3 % / Redundancy: 2.8 % / B_iso Wilson estimate: 62.07 Å² / CC_1/2: 0.993 / R_pim(I) all: 0.093 / Net I/σ(I): 6.3
Reflection shell	Resolution: 2.5→2.59 Å / Num. unique obs: 4288 / CC_1/2: 0.661 / R_pim(I) all: 0.684

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Processing

Software

Name	Version	Classification
PDB_EXTRACT	dev_3908	data extraction
PHENIX	dev_3908	refinement
PHASER	dev_3908	phasing
Coot		model building
iMOSFLM		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3ffz

3ffz

Resolution: 2.5→70.42 Å / SU ML: 0.3867 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2411	3755	4.97 %
R_work	0.2264	71760	-
obs	0.2271	41851	89.71 %

Solvent computation

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

Displacement parameters

B_iso mean: 70.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→70.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7287	0	16	65	7368

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0066	7461
X-RAY DIFFRACTION	f_angle_d	0.7976	10114
X-RAY DIFFRACTION	f_chiral_restr	0.0516	1128
X-RAY DIFFRACTION	f_plane_restr	0.005	1312
X-RAY DIFFRACTION	f_dihedral_angle_d	16.6345	2755

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 (%)
2.5-2.53	0.3197	133	0.3176	2456	X-RAY DIFFRACTION	83.9
2.53-2.56	0.3113	148	0.3265	2548	X-RAY DIFFRACTION	86.74
2.56-2.6	0.3224	154	0.3266	2672	X-RAY DIFFRACTION	89.15
2.6-2.64	0.4155	149	0.3438	2595	X-RAY DIFFRACTION	88.4
2.64-2.68	0.3358	133	0.3255	2604	X-RAY DIFFRACTION	88.92
2.68-2.72	0.3074	139	0.3364	2640	X-RAY DIFFRACTION	89.24
2.72-2.76	0.3434	141	0.3097	2707	X-RAY DIFFRACTION	89.34
2.76-2.81	0.4012	89	0.3158	2635	X-RAY DIFFRACTION	89.28
2.81-2.86	0.3734	162	0.303	2605	X-RAY DIFFRACTION	89.29
2.86-2.92	0.3565	126	0.3124	2704	X-RAY DIFFRACTION	88.47
2.92-2.98	0.3012	142	0.3178	2583	X-RAY DIFFRACTION	88.53
2.98-3.04	0.3256	135	0.3028	2616	X-RAY DIFFRACTION	89.23
3.04-3.11	0.3716	146	0.3127	2691	X-RAY DIFFRACTION	89.1
3.11-3.19	0.2835	141	0.3152	2613	X-RAY DIFFRACTION	89.5
3.19-3.28	0.3088	127	0.3018	2645	X-RAY DIFFRACTION	89.25
3.28-3.37	0.2704	151	0.2763	2663	X-RAY DIFFRACTION	89.82
3.37-3.48	0.301	144	0.2657	2630	X-RAY DIFFRACTION	89.25
3.48-3.61	0.2496	96	0.2413	2606	X-RAY DIFFRACTION	86.57
3.61-3.75	0.225	152	0.2404	2553	X-RAY DIFFRACTION	87.15
3.75-3.92	0.276	156	0.2183	2773	X-RAY DIFFRACTION	94.3
3.92-4.13	0.2253	173	0.2017	2818	X-RAY DIFFRACTION	94.47
4.13-4.39	0.1975	139	0.1781	2784	X-RAY DIFFRACTION	94.9
4.39-4.72	0.1769	114	0.16	2828	X-RAY DIFFRACTION	94.02
4.72-5.2	0.1813	145	0.1706	2756	X-RAY DIFFRACTION	93.19
5.2-5.95	0.1977	140	0.1902	2770	X-RAY DIFFRACTION	92.91
5.95-7.5	0.2121	131	0.2117	2543	X-RAY DIFFRACTION	85.65
7.5-70.42	0.1631	149	0.1631	2722	X-RAY DIFFRACTION	91.9

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	2.34575885624	0.444090748879	0.919920888145	-0.176100336925	0.00524748560092	0.62482121008	-0.242866454469	0.222870879584	-0.320201505808	0.140235674561	0.0507580948342	0.274214153335	0.644366842292	-0.157302112562	-0.00227062816821	1.0957270404	-0.261436035147	0.175386139085	0.539047887843	-0.140820549767	0.632616884533	73.014487106	-51.7903002758	14.2538921265
2	2.4740327533	-0.0993077065999	-0.555496339475	0.765782588542	0.110772292394	2.56281152376	-0.403348420149	0.204764504112	-0.0180410374583	0.0889729188056	0.00239150065604	0.0871706568207	0.943428089811	-0.0611326976675	-0.475770813214	0.979586653771	-0.136198821209	0.154746000112	0.497964191125	-0.0629079362945	0.477448298513	80.660208211	-48.9110897928	15.4426571692
3	0.0703245992689	-0.372906752262	-0.836074535439	0.478905273914	-0.609658242673	1.56589325009	0.0571917083273	-0.0998183881956	0.063632785921	-0.127362377225	-0.0772153252007	0.0603027501817	0.0500848581177	0.083331236207	-2.9720499267E-8	0.534972332727	-0.0546214623684	-0.020747593968	0.489823517193	-0.0916364822302	0.518409947177	81.8580046933	-35.6602492591	30.3561653635
4	1.00343892613	1.06379122315	-0.485167412676	0.901737051245	-0.571512370849	0.215253414134	-0.462138731193	-0.188921611535	0.138903635345	0.010601157108	0.122933980216	-0.237278922511	0.736288408805	0.675338422426	-0.104739863141	0.898758808144	0.218074469053	0.0269787111532	0.790676876161	0.0796103857145	0.485307369562	102.69082815	-46.9112444334	14.0873958161
5	1.46047945736	-0.846807325939	-0.652330344883	0.859488341211	-0.134251043667	1.50428788971	0.0540971231192	-0.139958019982	0.54437291995	0.0911862523597	0.0493523400242	0.0195266561556	0.141492963349	-0.0767468850576	0.0118911997302	0.629146155267	-0.0547886046522	-0.0578396189227	0.601019900228	-0.0276698031002	0.624346197833	79.9165445966	-30.8347001493	18.6062007967
6	0.545694803841	0.0950693800947	0.474983792082	-0.401051822183	0.210657980434	0.450454840271	-0.138978911809	0.0874482093807	-0.304784149903	-0.069884378323	0.125858464553	-0.0864987334668	0.219318158386	-0.132368713738	5.43388566887E-8	0.565110925321	-0.0933719390196	0.052136046506	0.523644843444	-0.00706308775652	0.526256813413	68.868311959	-38.9094260554	49.0993331382
7	0.416951250336	0.345548421143	-0.381862476647	-0.181802983745	-0.271092522317	0.710019495779	-0.403127364403	-0.275074472907	-0.0628602169998	-0.0304086775431	0.227186716943	0.0352100515003	0.363985153164	0.209608935081	-0.00217170001666	0.621583030937	-0.0363009734811	0.0646245568561	0.477523936716	-0.0244786978589	0.59452417852	83.3126757351	-39.8888979051	44.2070930946
8	0.871056390328	-0.549001330626	-0.114049857765	0.612544767504	0.0320835787844	1.10138272537	-0.0822930918625	-0.337502581132	0.208953333141	0.0406462973989	0.0799039796701	0.255581876701	-0.0354607273423	-0.217373798274	4.02792355278E-8	0.487729186158	-0.106689928807	0.0228055301753	0.532009740117	-0.0273739490045	0.658173486853	53.5103656746	-18.6606106562	56.2142336192
9	0.936335694115	-0.315306504948	-0.00901342542621	0.813317579883	-0.00228755705197	0.172771903273	0.0331583863754	-0.0182046159279	0.462013372684	0.0740046084329	0.0221616414144	0.00986964114483	-0.00144647402159	0.128930649331	2.97788043611E-8	0.466169121162	-0.0614199898691	-0.000728531680429	0.466902808237	-0.0692643036237	0.546043942755	89.6962980671	-21.1155962174	51.5222723826
10	2.32271859076	-0.552666417732	-0.233461523393	0.133591439472	0.139161564055	0.122627148798	-0.0533477249518	0.233483773429	0.37946246146	0.0226730138769	0.0487072218989	-0.00119265855599	0.000586706755124	0.0682922996783	5.66874965307E-10	0.451698226804	-0.0442754151146	-0.0106660929831	0.541735150797	0.0187708234506	0.537031847088	87.5633259707	-19.5116245542	42.8044719073
11	0.1074752227	-0.110146387867	-0.181472711644	0.456445750729	-0.0107370437435	0.347469520397	-0.0357007920294	-0.886070512465	-0.616130766959	0.129034954343	-0.263303388166	-0.120295304832	0.37458189914	0.0548855536231	-0.0185526517302	0.532020059476	-0.0270007558797	0.0363087545085	0.516619591255	-0.0311033216234	0.726393086423	130.310284751	-49.4286603697	54.3524448216
12	0.0720164947904	0.182921675764	-0.147370167485	0.138777848753	-0.289414470808	0.250186230967	0.208647633444	-0.442402032972	-0.0576430629678	0.561151548965	-0.128765548043	0.132388895197	0.366999395931	-0.664266018528	4.04423721056E-7	0.48799520341	-0.0306981952052	-0.0564722567449	0.574597075917	-0.0715327938687	0.559351764218	122.357496946	-40.3820490014	50.9268646938
13	0.0616439430159	-0.0491032410566	0.0284635276055	0.0044412485223	-0.0510525472259	0.0389756365524	-0.99865464092	0.328865279056	0.0716274063922	-0.00417080775856	-0.349212463304	-0.736716716746	0.00612850713203	0.620960762738	-0.500092530601	0.52666479016	-0.0911225410678	-0.0360391055292	0.508984888615	-0.0868596113856	0.627493657079	131.705286144	-35.0898522392	55.9938077349
14	0.427627709772	-0.506145844312	-0.174168874642	0.850956624672	-0.404667679772	0.843660886496	0.115792473147	0.371008218205	-0.0261731794469	-0.0724196875089	-0.146473920094	-0.253432030926	0.00181316267178	0.0756048007116	-9.06447483357E-8	0.476919861672	-0.00308338178097	-0.0360543075055	0.551432694865	-0.134315209598	0.632712518739	130.712297093	-42.1168162292	47.494871727
15	0.658851627112	0.121610755758	-0.667367719774	0.380031993309	-0.593321468365	1.02864683944	0.012213858086	-0.134642285556	-0.214899638112	-0.246439561018	-0.141389383992	-0.474688161689	0.252874135633	-0.301545688297	-0.00466239834425	0.473664430813	-0.0280805181405	-0.105639008715	0.569475340254	-0.0911619082273	0.569193881876	124.437030529	-36.6980261055	53.4568812301

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 65 )	A	A	1 - 65	1 - 65
2	2	chain 'A' and (resid 66 through 189 )	A	A	66 - 189	66 - 189
3	3	chain 'A' and (resid 190 through 264 )	A	A	190 - 264	190 - 264
4	4	chain 'A' and (resid 265 through 306 )	A	A	265 - 306	265 - 306
5	5	chain 'A' and (resid 307 through 395 )	A	A	307 - 395	307 - 395
6	6	chain 'A' and (resid 396 through 445 )	A	A	396 - 445	396 - 445
7	7	chain 'A' and (resid 446 through 526 )	A	A	446 - 526	446 - 488
8	8	chain 'A' and (resid 527 through 587 )	A	A	527 - 587	489 - 549
9	9	chain 'A' and (resid 588 through 659 )	A	A	588 - 659	550 - 621
10	10	chain 'A' and (resid 660 through 831 )	A	A	660 - 831	622 - 793
11	11	chain 'B' and (resid 2 through 24 )	B	B	2 - 24	1 - 23
12	12	chain 'B' and (resid 25 through 36 )	B	B	25 - 36	24 - 35
13	13	chain 'B' and (resid 37 through 48 )	B	B	37 - 48	36 - 47
14	14	chain 'B' and (resid 49 through 95 )	B	B	49 - 95	48 - 94
15	15	chain 'B' and (resid 96 through 123 )	B	B	96 - 123	95 - 122

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