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Basic information

Entry
Database: PDB / ID: 4lo2
TitleHA17-HA33-Lac
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 A (botA) / Toxicity of botulinum toxin type B (botB) / carbohydrate binding
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
beta-lactose / HA-33 / HA-17
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.254 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)85,9175
Polymers85,2333
Non-polymers6852
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-18 kcal/mol
Surface area30690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.490, 119.153, 163.071
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-237-

HOH

21B-453-

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)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 3.03 Å3/Da / Density % sol: 59.47 %
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: 2.254→50 Å / Num. all: 49187 / Num. obs: 47909 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.4
Reflection shellResolution: 2.254→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2 / % possible all: 98.9

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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: 2.254→32.06 Å / SU ML: 0.62 / σ(F): 1.35 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 2430 5.07 %RANDOM
Rwork0.1664 ---
obs0.1686 47909 97.31 %-
all-49187 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.888 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.1349 Å20 Å2-0 Å2
2---10.8823 Å20 Å2
3----2.2527 Å2
Refinement stepCycle: LAST / Resolution: 2.254→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5853 0 46 225 6124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086039
X-RAY DIFFRACTIONf_angle_d1.0498243
X-RAY DIFFRACTIONf_dihedral_angle_d13.4672168
X-RAY DIFFRACTIONf_chiral_restr0.078932
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.254-2.29960.23171430.18012634X-RAY DIFFRACTION96
2.2996-2.34960.20351550.17732706X-RAY DIFFRACTION99
2.3496-2.40420.27361470.18562644X-RAY DIFFRACTION98
2.4042-2.46440.24551350.19032582X-RAY DIFFRACTION96
2.4644-2.5310.22691470.19612717X-RAY DIFFRACTION100
2.531-2.60540.26311320.19492735X-RAY DIFFRACTION100
2.6054-2.68950.2461310.19892707X-RAY DIFFRACTION100
2.6895-2.78550.27231360.19012752X-RAY DIFFRACTION99
2.7855-2.8970.22191500.1732684X-RAY DIFFRACTION99
2.897-3.02870.22591420.1722711X-RAY DIFFRACTION99
3.0287-3.18830.24691400.17252631X-RAY DIFFRACTION96
3.1883-3.38780.21091530.17442695X-RAY DIFFRACTION99
3.3878-3.64910.18971570.15742740X-RAY DIFFRACTION99
3.6491-4.01570.20171390.15422733X-RAY DIFFRACTION99
4.0157-4.59530.16531580.1312636X-RAY DIFFRACTION96
4.5953-5.7840.18481410.14222729X-RAY DIFFRACTION97
5.784-32.06310.23751240.20092443X-RAY DIFFRACTION84
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)
11.85160.2937-0.44163.83231.96844.28970.06630.0177-0.06590.078-0.0792-0.05010.3187-0.00740.00730.20410.01-0.02560.22090.02440.250136.1354-12.773948.0501
25.4149-0.50750.18984.00451.10254.8235-0.00640.55170.0794-0.30050.1077-0.04330.01260.0052-0.09950.2873-0.0429-0.01780.31110.01110.254840.3045-25.065117.4059
32.12590.529-0.47813.9043-0.05871.9012-0.1888-0.3821-0.1280.8963-0.3333-0.2928-0.49440.59650.37390.5531-0.1129-0.09660.4771-0.02370.437649.50111.590981.7664
44.87030.0083-0.86785.89610.95355.0838-0.05570.11940.9806-0.14530.3254-0.5202-0.83530.6488-0.17710.4311-0.1453-0.0170.37190.00690.350650.118917.626164.4808
53.93972.9423-3.21388.3313-4.50428.36570.4681-0.48640.62870.5866-0.1989-0.3367-1.17830.7225-0.1870.5845-0.0893-0.13930.3786-0.08040.487147.93819.727376.2446
62.4135-0.19470.78237.6431-4.11987.9064-0.0343-0.51050.14850.25620.18280.5432-0.3052-0.2289-0.02840.48760.0503-0.02020.3492-0.04370.267939.227110.565181.6737
72.7570.08970.70462.90512.07095.6184-0.13-0.26560.42750.3236-0.13360.2603-0.9435-0.40750.20650.42040.0221-0.0130.3218-0.05540.389535.770116.423571.2119
86.5376-1.23720.33154.30360.41273.03780.2887-0.2261-0.11090.5101-0.0837-0.48470.20120.5279-0.07170.37620.0238-0.08560.3243-0.0040.273947.54474.292775.096
94.0930.62690.39777.72820.78899.1791-0.284-0.34720.1040.0197-0.16470.53380.3897-0.69290.3880.20060.01710.00420.2431-0.0370.26936.19862.321168.5941
101.5748-0.29670.29694.0611-0.9923.0614-0.17050.2726-0.0251-0.1157-0.0611-0.65630.03780.53040.21630.1977-0.04380.02870.3521-0.00940.273647.78025.749460.8808
113.68976.44915.62152.04559.93798.67950.2017-0.2910.16830.35960.1213-0.8679-0.0190.4494-0.2680.3789-0.0447-0.16730.46540.00340.459652.35758.999371.1196
123.3315-0.84091.12072.48830.07513.74420.06310.09290.1479-0.2807-0.07210.0496-0.5162-0.0251-0.00110.27620.02460.02820.16080.00220.230834.431315.58141.729
134.7321-1.67040.73622.75570.84362.32060.93391.4264-0.8659-0.8378-0.77330.30350.54540.188-0.11720.65610.2707-0.15950.686-0.18340.558310.93214.80217.2986
143.4421-2.5721.78464.25340.57143.83390.98781.7174-0.3273-1.115-0.763-0.13670.30680.4569-0.09991.00030.5316-0.01931.0999-0.12260.57118.875213.236312.5903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:150)
2X-RAY DIFFRACTION2chain 'A' and (resseq 151:294)
3X-RAY DIFFRACTION3chain 'C' and (resseq 3:17)
4X-RAY DIFFRACTION4chain 'C' and (resseq 18:36)
5X-RAY DIFFRACTION5chain 'C' and (resseq 37:50)
6X-RAY DIFFRACTION6chain 'C' and (resseq 51:60)
7X-RAY DIFFRACTION7chain 'C' and (resseq 61:86)
8X-RAY DIFFRACTION8chain 'C' and (resseq 87:101)
9X-RAY DIFFRACTION9chain 'C' and (resseq 102:113)
10X-RAY DIFFRACTION10chain 'C' and (resseq 114:136)
11X-RAY DIFFRACTION11chain 'C' and (resseq 137:146)
12X-RAY DIFFRACTION12chain 'B' and (resseq 9:150)
13X-RAY DIFFRACTION13chain 'B' and (resseq 151:222)
14X-RAY DIFFRACTION14chain 'B' and (resseq 223:294)

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