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- PDB-7k7y: Crystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E9 -

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Basic information

Entry
Database: PDB / ID: 7k7y
TitleCrystal structure of BoNT/E LC-HN domain in complex with VHH JLE-E9
Components
  • Botulinum neurotoxin type E
  • JLE-E9
KeywordsANTITOXIN / 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 ...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 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / 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
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: 3.6 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 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type E
D: JLE-E9
E: Botulinum neurotoxin type E
G: Botulinum neurotoxin type E
B: Botulinum neurotoxin type E
C: JLE-E9
F: JLE-E9
H: JLE-E9


Theoretical massNumber of molelcules
Total (without water)443,2698
Polymers443,2698
Non-polymers00
Water0
1
A: Botulinum neurotoxin type E
D: JLE-E9


Theoretical massNumber of molelcules
Total (without water)110,8172
Polymers110,8172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Botulinum neurotoxin type E
F: JLE-E9


Theoretical massNumber of molelcules
Total (without water)110,8172
Polymers110,8172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Botulinum neurotoxin type E
H: JLE-E9


Theoretical massNumber of molelcules
Total (without water)110,8172
Polymers110,8172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Botulinum neurotoxin type E
C: JLE-E9


Theoretical massNumber of molelcules
Total (without water)110,8172
Polymers110,8172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.035, 208.650, 210.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROTHRTHR(chain 'A' and (resid 2 through 15 or (resid 16...AA2 - 4577 - 462
121TYRTYRASNASN(chain 'A' and (resid 2 through 15 or (resid 16...AA501 - 504506 - 509
131THRTHRILEILE(chain 'A' and (resid 2 through 15 or (resid 16...AA506 - 650511 - 655
141LYSLYSGLNGLN(chain 'A' and (resid 2 through 15 or (resid 16...AA660 - 799665 - 804
151SERSERTYRTYR(chain 'A' and (resid 2 through 15 or (resid 16...AA807 - 830812 - 835
211PROPROTHRTHR(chain 'B' and (resid 2 through 15 or (resid 16...BE2 - 4577 - 462
221TYRTYRASNASN(chain 'B' and (resid 2 through 15 or (resid 16...BE501 - 504506 - 509
231THRTHRILEILE(chain 'B' and (resid 2 through 15 or (resid 16...BE506 - 650511 - 655
241LYSLYSGLNGLN(chain 'B' and (resid 2 through 15 or (resid 16...BE660 - 799665 - 804
251SERSERTYRTYR(chain 'B' and (resid 2 through 15 or (resid 16...BE807 - 830812 - 835
311PROPROTHRTHR(chain 'E' and (resid 2 through 134 or (resid 135...EC2 - 4577 - 462
321TYRTYRASNASN(chain 'E' and (resid 2 through 134 or (resid 135...EC501 - 504506 - 509
331THRTHRILEILE(chain 'E' and (resid 2 through 134 or (resid 135...EC506 - 650511 - 655
341LYSLYSGLNGLN(chain 'E' and (resid 2 through 134 or (resid 135...EC660 - 799665 - 804
351SERSERTYRTYR(chain 'E' and (resid 2 through 134 or (resid 135...EC807 - 830812 - 835
411PROPROTHRTHR(chain 'G' and (resid 2 through 15 or (resid 16...GD2 - 4577 - 462
421TYRTYRASNASN(chain 'G' and (resid 2 through 15 or (resid 16...GD501 - 504506 - 509
431THRTHRILEILE(chain 'G' and (resid 2 through 15 or (resid 16...GD506 - 650511 - 655
441LYSLYSGLNGLN(chain 'G' and (resid 2 through 15 or (resid 16...GD660 - 799665 - 804
451SERSERTYRTYR(chain 'G' and (resid 2 through 15 or (resid 16...GD807 - 830812 - 835
112GLNGLNGLYGLY(chain 'C' and (resid 1 through 9 or (resid 12...CF1 - 86 - 13
122VALVALVALVAL(chain 'C' and (resid 1 through 9 or (resid 12...CF12 - 12017 - 125
212GLNGLNGLYGLY(chain 'D' and ((resid 1 and (name N or name...DB1 - 86 - 13
222VALVALVALVAL(chain 'D' and ((resid 1 and (name N or name...DB12 - 12017 - 125
312GLNGLNGLYGLYchain 'F'FG1 - 86 - 13
322VALVALVALVALchain 'F'FG12 - 12017 - 125
412GLNGLNGLYGLY(chain 'H' and (resid 1 through 9 or (resid 12...HH1 - 86 - 13
422VALVALVALVAL(chain 'H' and (resid 1 through 9 or (resid 12...HH12 - 12017 - 125

NCS ensembles :
ID
1
2

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Components

#1: Protein
Botulinum neurotoxin type E


Mass: 96816.734 Da / Num. of mol.: 4
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: Antibody
JLE-E9


Mass: 14000.442 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 12 % PEG 20K, 0.1 M sodium citrate pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 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: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3.6→148.19 Å / Num. obs: 55326 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 125.48 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.11 / Net I/σ(I): 6.6
Reflection shellResolution: 3.6→3.7 Å / Num. unique obs: 4534 / CC1/2: 0.309 / Rpim(I) all: 0.96

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Processing

Software
NameVersionClassification
PHENIXmodel building
REFMACv5.7refinement
MOSFLMdata processing
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ffz

3ffz


Resolution: 3.6→74.09 Å / SU ML: 0.625 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.8104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2877 4992 4.91 %
Rwork0.2614 96714 -
obs0.2627 55219 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 123.89 Å2
Refinement stepCycle: LAST / Resolution: 3.6→74.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28699 0 0 0 28699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002229252
X-RAY DIFFRACTIONf_angle_d0.518439646
X-RAY DIFFRACTIONf_chiral_restr0.04214449
X-RAY DIFFRACTIONf_plane_restr0.0035156
X-RAY DIFFRACTIONf_dihedral_angle_d13.354110758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.640.43251410.40073213X-RAY DIFFRACTION93.58
3.64-3.680.41471310.3863227X-RAY DIFFRACTION93.64
3.68-3.730.36141860.37553155X-RAY DIFFRACTION94.25
3.73-3.780.31611790.37083217X-RAY DIFFRACTION94.78
3.78-3.830.40811440.3633261X-RAY DIFFRACTION94.53
3.83-3.880.41691680.37073225X-RAY DIFFRACTION93.96
3.88-3.930.34651930.36423114X-RAY DIFFRACTION93.39
3.93-3.990.38441670.35113192X-RAY DIFFRACTION92.59
3.99-4.050.36091280.33593139X-RAY DIFFRACTION91.21
4.05-4.120.34031380.31533094X-RAY DIFFRACTION92.11
4.12-4.190.351690.31313339X-RAY DIFFRACTION96.75
4.19-4.270.31681700.30613319X-RAY DIFFRACTION97.57
4.27-4.350.31641780.29733323X-RAY DIFFRACTION97.25
4.35-4.440.32761610.29593312X-RAY DIFFRACTION96.77
4.44-4.540.3191890.2923274X-RAY DIFFRACTION97
4.54-4.640.31531940.27833260X-RAY DIFFRACTION96.4
4.64-4.760.27211700.25753252X-RAY DIFFRACTION96.34
4.76-4.890.2851340.25563309X-RAY DIFFRACTION96.04
4.89-5.030.28571600.25583365X-RAY DIFFRACTION97.21
5.03-5.190.30761640.26853283X-RAY DIFFRACTION96.64
5.19-5.380.28621760.26643241X-RAY DIFFRACTION95.55
5.38-5.590.26491900.27073110X-RAY DIFFRACTION92.7
5.59-5.850.24631870.26513061X-RAY DIFFRACTION90.37
5.85-6.160.30612040.26083052X-RAY DIFFRACTION90.7
6.16-6.540.25971570.25843318X-RAY DIFFRACTION96.82
6.54-7.050.25751740.24483277X-RAY DIFFRACTION96.78
7.05-7.750.23741950.22943246X-RAY DIFFRACTION95.56
7.75-8.870.21811230.19223280X-RAY DIFFRACTION95.43
8.87-11.170.20121620.16543167X-RAY DIFFRACTION92.78
11.17-74.090.26961600.20973089X-RAY DIFFRACTION90.58

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