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Basic information

Entry
Database: PDB / ID: 4lo3
TitleHA17-HA33-LacNac
Components
  • HA-17
  • HA-33
KeywordsPROTEIN TRANSPORT / progenitor toxin complex / botulinum neurotoxin / botulism / neurotoxin associated protein / hemagglutinin / carbohydrate/sugar binding / secreted protein
Function / homology
Function and homology information


Toxicity of botulinum toxin type B (botB) / Toxicity of botulinum toxin type A (botA)
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-lactosamine / HA-33 / HA-17
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsLee, K. / Gu, S. / Jin, L. / Le, T.T. / Cheng, L.W. / Strotmeier, J. / Kruel, A.M. / Yao, G. / Perry, K. / Rummel, A. / Jin, R.
CitationJournal: PLoS Pathog / Year: 2013
Title: Structure of a bimodular botulinum neurotoxin complex provides insights into its oral toxicity.
Authors: Kwangkook Lee / Shenyan Gu / Lei Jin / Thi Tuc Nghi Le / Luisa W Cheng / Jasmin Strotmeier / Anna Magdalena Kruel / Guorui Yao / Kay Perry / Andreas Rummel / Rongsheng Jin /
Abstract: Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the fatal disease botulism, a flaccid paralysis of the muscle. BoNTs are released together with several auxiliary ...Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the fatal disease botulism, a flaccid paralysis of the muscle. BoNTs are released together with several auxiliary proteins as progenitor toxin complexes (PTCs) to become highly potent oral poisons. Here, we report the structure of a ∼760 kDa 14-subunit large PTC of serotype A (L-PTC/A) and reveal insight into its absorption mechanism. Using a combination of X-ray crystallography, electron microscopy, and functional studies, we found that L-PTC/A consists of two structurally and functionally independent sub-complexes. A hetero-dimeric 290 kDa complex protects BoNT, while a hetero-dodecameric 470 kDa complex facilitates its absorption in the harsh environment of the gastrointestinal tract. BoNT absorption is mediated by nine glycan-binding sites on the dodecameric sub-complex that forms multivalent interactions with carbohydrate receptors on intestinal epithelial cells. We identified monosaccharides that blocked oral BoNT intoxication in mice, which suggests a new strategy for the development of preventive countermeasures for BoNTs based on carbohydrate receptor mimicry.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HA-33
C: HA-17
B: HA-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9995
Polymers85,2333
Non-polymers7672
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-19 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.216, 118.803, 162.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-258-

HOH

21B-459-

HOH

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Components

#1: Protein HA-33 / HA-33 protein / HA34 / Non-toxin haemagglutinin HA34


Mass: 34081.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-33, ha33, ha34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45871
#2: Protein HA-17 / HA-17 protein / HA17 / Ha17 protein / Non-toxin haemagglutinin HA17


Mass: 17069.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha17, HA-17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45878
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.2
Details: 0.1 M MES, 0.1 M magnesium chloride, 5% PEG8000, pH 6.2, EVAPORATION, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. all: 49590 / Num. obs: 49357 / % possible obs: 99.53 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.5
Reflection shellResolution: 2.249→2.4 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→47.956 Å / SU ML: 0.73 / σ(F): 1.36 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 2505 5.08 %RANDOM
Rwork0.1791 ---
obs0.1808 49357 99.53 %-
all-49590 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.472 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.9113 Å2-0 Å2-0 Å2
2---10.3061 Å20 Å2
3----5.6052 Å2
Refinement stepCycle: LAST / Resolution: 2.249→47.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 52 217 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096037
X-RAY DIFFRACTIONf_angle_d1.0888240
X-RAY DIFFRACTIONf_dihedral_angle_d14.7962181
X-RAY DIFFRACTIONf_chiral_restr0.223931
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.29180.31641270.23322524X-RAY DIFFRACTION97
2.2918-2.33860.27311380.21132568X-RAY DIFFRACTION100
2.3386-2.38950.30521460.21212566X-RAY DIFFRACTION100
2.3895-2.44510.26891390.2172573X-RAY DIFFRACTION99
2.4451-2.50620.2711360.21072582X-RAY DIFFRACTION100
2.5062-2.5740.24111330.21852597X-RAY DIFFRACTION100
2.574-2.64970.29071290.21642573X-RAY DIFFRACTION99
2.6497-2.73520.261490.21262575X-RAY DIFFRACTION100
2.7352-2.8330.27171400.20292608X-RAY DIFFRACTION100
2.833-2.94640.23851530.18822576X-RAY DIFFRACTION100
2.9464-3.08040.21441590.18312599X-RAY DIFFRACTION100
3.0804-3.24280.22681290.18282604X-RAY DIFFRACTION100
3.2428-3.44590.22161380.18542597X-RAY DIFFRACTION99
3.4459-3.71190.19751370.17292634X-RAY DIFFRACTION100
3.7119-4.08530.19951430.16652627X-RAY DIFFRACTION100
4.0853-4.6760.17161280.13712643X-RAY DIFFRACTION100
4.676-5.88960.16991240.15042663X-RAY DIFFRACTION99
5.8896-47.96740.18221570.19292743X-RAY DIFFRACTION99
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)
11.14980.101-0.20173.76371.82474.20730.05280.0467-0.10860.0843-0.10160.07030.2873-0.0540.04680.16030.0027-0.01930.23030.01750.259836.5124-12.858847.8465
24.6727-0.19560.4623.68350.59174.85560.01090.73850.1061-0.36460.1835-0.29740.11640.4532-0.20620.3198-0.02320.00550.4361-0.01520.337245.309-25.368517.574
34.9533-0.39020.50934.21080.67215.51790.01170.39140.0616-0.28130.10710.22470.2138-0.3502-0.09960.4023-0.0479-0.06050.39580.01640.367336.0117-25.01517.0943
42.22380.4114-1.24952.9807-0.21524.3407-0.2371-0.50450.2060.5572-0.0914-0.2622-0.39580.89370.31260.4932-0.0737-0.12420.4794-0.00950.392449.816911.553881.4324
53.3210.2442-1.21844.3951.1365.74470.02150.04410.65820.19220.2545-0.6821-1.13970.7454-0.21650.4977-0.172-0.07910.37720.01740.405351.118619.634666.233
61.4231.4928-0.38022.4987-1.59395.81860.1116-0.31180.29210.5694-0.15250.2645-0.5821-0.12580.08230.49040.0814-0.12580.3287-0.04590.287140.749111.037782.7413
73.66081.0609-1.01562.001-3.97324.8843-0.3028-0.22160.36460.06330.35260.054-0.5013-0.4291-0.0780.5906-0.0043-0.04830.3813-0.05430.291342.302917.689977.1411
81.6710.73980.6072.10091.41955.0227-0.085-0.22240.38160.2528-0.1880.3591-0.9453-0.29510.2260.40950.0125-0.02080.2604-0.05220.314536.23916.295568.4944
92.7351-1.2897-0.06074.90690.11714.2643-0.0156-0.13820.14420.4769-0.0617-0.083-0.0264-0.12250.14510.30110.0041-0.00050.2710.00840.230740.67335.348472.5196
101.4849-0.1060.64944.066-0.97113.1918-0.22070.3460.0522-0.2609-0.0257-0.5508-0.00040.50140.25050.2373-0.0410.02350.40630.00680.328248.05645.654260.6328
112.65584.86873.56998.95986.57484.81950.0566-0.05790.29910.46690.0979-0.6029-0.00120.5756-0.18480.3526-0.0324-0.12060.48730.01740.451552.62798.965270.7717
123.5231-0.62141.14732.5215-0.45223.86130.03990.14240.1707-0.2019-0.11260.0604-0.5371-0.02770.05850.27680.04550.01040.17470.00750.243834.540115.497141.5702
135.6576-1.87110.9693.33981.042.59260.95121.2357-0.7376-0.9417-0.74770.45440.5585-0.0507-0.15220.69230.2805-0.18210.6888-0.17770.607211.020414.975717.6297
144.5458-2.51471.4692.49220.69742.6370.91221.6201-0.4578-1.2248-0.79580.03870.29020.3111-0.1331.14220.583-0.07671.0777-0.15360.767118.878913.033212.2975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:150)
2X-RAY DIFFRACTION2chain 'A' and (resseq 151:222)
3X-RAY DIFFRACTION3chain 'A' and (resseq 223:294)
4X-RAY DIFFRACTION4chain 'C' and (resseq 3:17)
5X-RAY DIFFRACTION5chain 'C' and (resseq 18:44)
6X-RAY DIFFRACTION6chain 'C' and (resseq 45:54)
7X-RAY DIFFRACTION7chain 'C' and (resseq 55:63)
8X-RAY DIFFRACTION8chain 'C' and (resseq 64:79)
9X-RAY DIFFRACTION9chain 'C' and (resseq 80:113)
10X-RAY DIFFRACTION10chain 'C' and (resseq 114:136)
11X-RAY DIFFRACTION11chain 'C' and (resseq 137:146)
12X-RAY DIFFRACTION12chain 'B' and (resseq 10:150)
13X-RAY DIFFRACTION13chain 'B' and (resseq 151:219)
14X-RAY DIFFRACTION14chain 'B' and (resseq 220:294)

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