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

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Basic information

Entry
Database: PDB / ID: 7k84
TitleCrystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E5
Components
  • Botulinum neurotoxin type E
  • JLE-E5
KeywordsANTITOXIN / Botulinum neurotoxin (BoNT) / VHH / receptor-binding domain / TOXIN
Function / homology
Function and homology information


Toxicity of botulinum toxin type E (botE) / bontoxilysin / negative regulation of neurotransmitter secretion / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding ...Toxicity of botulinum toxin type E (botE) / bontoxilysin / negative regulation of neurotransmitter secretion / 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 / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type E / Botulinum neurotoxin type E
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLam, K. / Jin, R.
Funding support United States, 4items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionSep 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type E
B: JLE-E5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,1526
Polymers110,7982
Non-polymers3544
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-87 kcal/mol
Surface area40320 Å2
MethodPISA
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 number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

#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 interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→131.04 Å / Num. obs: 43226 / % possible obs: 96.3 % / Redundancy: 2.8 % / Biso Wilson estimate: 62.07 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.093 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 4288 / CC1/2: 0.661 / Rpim(I) all: 0.684

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Processing

Software
NameVersionClassification
PDB_EXTRACTdev_3908data extraction
PHENIXdev_3908refinement
PHASERdev_3908phasing
Cootmodel building
iMOSFLMdata reduction
Aimlessdata scaling
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2411 3755 4.97 %
Rwork0.2264 71760 -
obs0.2271 41851 89.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→70.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7287 0 16 65 7368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00667461
X-RAY DIFFRACTIONf_angle_d0.797610114
X-RAY DIFFRACTIONf_chiral_restr0.05161128
X-RAY DIFFRACTIONf_plane_restr0.0051312
X-RAY DIFFRACTIONf_dihedral_angle_d16.63452755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.31971330.31762456X-RAY DIFFRACTION83.9
2.53-2.560.31131480.32652548X-RAY DIFFRACTION86.74
2.56-2.60.32241540.32662672X-RAY DIFFRACTION89.15
2.6-2.640.41551490.34382595X-RAY DIFFRACTION88.4
2.64-2.680.33581330.32552604X-RAY DIFFRACTION88.92
2.68-2.720.30741390.33642640X-RAY DIFFRACTION89.24
2.72-2.760.34341410.30972707X-RAY DIFFRACTION89.34
2.76-2.810.4012890.31582635X-RAY DIFFRACTION89.28
2.81-2.860.37341620.3032605X-RAY DIFFRACTION89.29
2.86-2.920.35651260.31242704X-RAY DIFFRACTION88.47
2.92-2.980.30121420.31782583X-RAY DIFFRACTION88.53
2.98-3.040.32561350.30282616X-RAY DIFFRACTION89.23
3.04-3.110.37161460.31272691X-RAY DIFFRACTION89.1
3.11-3.190.28351410.31522613X-RAY DIFFRACTION89.5
3.19-3.280.30881270.30182645X-RAY DIFFRACTION89.25
3.28-3.370.27041510.27632663X-RAY DIFFRACTION89.82
3.37-3.480.3011440.26572630X-RAY DIFFRACTION89.25
3.48-3.610.2496960.24132606X-RAY DIFFRACTION86.57
3.61-3.750.2251520.24042553X-RAY DIFFRACTION87.15
3.75-3.920.2761560.21832773X-RAY DIFFRACTION94.3
3.92-4.130.22531730.20172818X-RAY DIFFRACTION94.47
4.13-4.390.19751390.17812784X-RAY DIFFRACTION94.9
4.39-4.720.17691140.162828X-RAY DIFFRACTION94.02
4.72-5.20.18131450.17062756X-RAY DIFFRACTION93.19
5.2-5.950.19771400.19022770X-RAY DIFFRACTION92.91
5.95-7.50.21211310.21172543X-RAY DIFFRACTION85.65
7.5-70.420.16311490.16312722X-RAY DIFFRACTION91.9
Refinement TLS params.

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

IDL11 (°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)
12.345758856240.4440907488790.919920888145-0.1761003369250.005247485600920.62482121008-0.2428664544690.222870879584-0.3202015058080.1402356745610.05075809483420.2742141533350.644366842292-0.157302112562-0.002270628168211.0957270404-0.2614360351470.1753861390850.539047887843-0.1408205497670.63261688453373.014487106-51.790300275814.2538921265
22.4740327533-0.0993077065999-0.5554963394750.7657825885420.1107722923942.56281152376-0.4033484201490.204764504112-0.01804103745830.08897291880560.002391500656040.08717065682070.943428089811-0.0611326976675-0.4757708132140.979586653771-0.1361988212090.1547460001120.497964191125-0.06290793629450.47744829851380.660208211-48.911089792815.4426571692
30.0703245992689-0.372906752262-0.8360745354390.478905273914-0.6096582426731.565893250090.0571917083273-0.09981838819560.063632785921-0.127362377225-0.07721532520070.06030275018170.05008485811770.083331236207-2.9720499267E-80.534972332727-0.0546214623684-0.0207475939680.489823517193-0.09163648223020.51840994717781.8580046933-35.660249259130.3561653635
41.003438926131.06379122315-0.4851674126760.901737051245-0.5715123708490.215253414134-0.462138731193-0.1889216115350.1389036353450.0106011571080.122933980216-0.2372789225110.7362884088050.675338422426-0.1047398631410.8987588081440.2180744690530.02697871115320.7906768761610.07961038571450.485307369562102.69082815-46.911244433414.0873958161
51.46047945736-0.846807325939-0.6523303448830.859488341211-0.1342510436671.504287889710.0540971231192-0.1399580199820.544372919950.09118625235970.04935234002420.01952665615560.141492963349-0.07674688505760.01189119973020.629146155267-0.0547886046522-0.05783961892270.601019900228-0.02766980310020.62434619783379.9165445966-30.834700149318.6062007967
60.5456948038410.09506938009470.474983792082-0.4010518221830.2106579804340.450454840271-0.1389789118090.0874482093807-0.304784149903-0.0698843783230.125858464553-0.08649873346680.219318158386-0.1323687137385.43388566887E-80.565110925321-0.09337193901960.0521360465060.523644843444-0.007063087756520.52625681341368.868311959-38.909426055449.0993331382
70.4169512503360.345548421143-0.381862476647-0.181802983745-0.2710925223170.710019495779-0.403127364403-0.275074472907-0.0628602169998-0.03040867754310.2271867169430.03521005150030.3639851531640.209608935081-0.002171700016660.621583030937-0.03630097348110.06462455685610.477523936716-0.02447869785890.5945241785283.3126757351-39.888897905144.2070930946
80.871056390328-0.549001330626-0.1140498577650.6125447675040.03208357878441.10138272537-0.0822930918625-0.3375025811320.2089533331410.04064629739890.07990397967010.255581876701-0.0354607273423-0.2173737982744.02792355278E-80.487729186158-0.1066899288070.02280553017530.532009740117-0.02737394900450.65817348685353.5103656746-18.660610656256.2142336192
90.936335694115-0.315306504948-0.009013425426210.813317579883-0.002287557051970.1727719032730.0331583863754-0.01820461592790.4620133726840.07400460843290.02216164141440.00986964114483-0.001446474021590.1289306493312.97788043611E-80.466169121162-0.0614199898691-0.0007285316804290.466902808237-0.06926430362370.54604394275589.6962980671-21.115596217451.5222723826
102.32271859076-0.552666417732-0.2334615233930.1335914394720.1391615640550.122627148798-0.05334772495180.2334837734290.379462461460.02267301387690.0487072218989-0.001192658555990.0005867067551240.06829229967835.66874965307E-100.451698226804-0.0442754151146-0.01066609298310.5417351507970.01877082345060.53703184708887.5633259707-19.511624554242.8044719073
110.1074752227-0.110146387867-0.1814727116440.456445750729-0.01073704374350.347469520397-0.0357007920294-0.886070512465-0.6161307669590.129034954343-0.263303388166-0.1202953048320.374581899140.0548855536231-0.01855265173020.532020059476-0.02700075587970.03630875450850.516619591255-0.03110332162340.726393086423130.310284751-49.428660369754.3524448216
120.07201649479040.182921675764-0.1473701674850.138777848753-0.2894144708080.2501862309670.208647633444-0.442402032972-0.05764306296780.561151548965-0.1287655480430.1323888951970.366999395931-0.6642660185284.04423721056E-70.48799520341-0.0306981952052-0.05647225674490.574597075917-0.07153279386870.559351764218122.357496946-40.382049001450.9268646938
130.0616439430159-0.04910324105660.02846352760550.0044412485223-0.05105254722590.0389756365524-0.998654640920.3288652790560.0716274063922-0.00417080775856-0.349212463304-0.7367167167460.006128507132030.620960762738-0.5000925306010.52666479016-0.0911225410678-0.03603910552920.508984888615-0.08685961138560.627493657079131.705286144-35.089852239255.9938077349
140.427627709772-0.506145844312-0.1741688746420.850956624672-0.4046676797720.8436608864960.1157924731470.371008218205-0.0261731794469-0.0724196875089-0.146473920094-0.2534320309260.001813162671780.0756048007116-9.06447483357E-80.476919861672-0.00308338178097-0.03605430750550.551432694865-0.1343152095980.632712518739130.712297093-42.116816229247.494871727
150.6588516271120.121610755758-0.6673677197740.380031993309-0.5933214683651.028646839440.012213858086-0.134642285556-0.214899638112-0.246439561018-0.141389383992-0.4746881616890.252874135633-0.301545688297-0.004662398344250.473664430813-0.0280805181405-0.1056390087150.569475340254-0.09116190822730.569193881876124.437030529-36.698026105553.4568812301
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 65 )AA1 - 651 - 65
22chain 'A' and (resid 66 through 189 )AA66 - 18966 - 189
33chain 'A' and (resid 190 through 264 )AA190 - 264190 - 264
44chain 'A' and (resid 265 through 306 )AA265 - 306265 - 306
55chain 'A' and (resid 307 through 395 )AA307 - 395307 - 395
66chain 'A' and (resid 396 through 445 )AA396 - 445396 - 445
77chain 'A' and (resid 446 through 526 )AA446 - 526446 - 488
88chain 'A' and (resid 527 through 587 )AA527 - 587489 - 549
99chain 'A' and (resid 588 through 659 )AA588 - 659550 - 621
1010chain 'A' and (resid 660 through 831 )AA660 - 831622 - 793
1111chain 'B' and (resid 2 through 24 )BB2 - 241 - 23
1212chain 'B' and (resid 25 through 36 )BB25 - 3624 - 35
1313chain 'B' and (resid 37 through 48 )BB37 - 4836 - 47
1414chain 'B' and (resid 49 through 95 )BB49 - 9548 - 94
1515chain 'B' and (resid 96 through 123 )BB96 - 12395 - 122

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