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- PDB-4lo1: HA17-HA33-Gal -

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Basic information

Entry
Database: PDB / ID: 4lo1
TitleHA17-HA33-Gal
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
beta-D-galactopyranose / 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 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 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)85,5935
Polymers85,2333
Non-polymers3602
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-20 kcal/mol
Surface area30260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.131, 118.697, 162.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 59.4 %
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: APS / Beamline: 24-ID-C / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2011
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.254→47.9 Å / Num. all: 49045 / Num. obs: 48977 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.5
Reflection shellResolution: 2.254→2.4 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
JBluIce-EPICSdata 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→36.169 Å / SU ML: 0.83 / σ(F): 1.35 / Phase error: 25.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 2480 5.06 %RANDOM
Rwork0.1985 ---
obs0.1999 48977 99.66 %-
all-49045 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.164 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.0969 Å2-0 Å2-0 Å2
2---15.2563 Å2-0 Å2
3----5.8406 Å2
Refinement stepCycle: LAST / Resolution: 2.254→36.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 24 236 6105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036009
X-RAY DIFFRACTIONf_angle_d0.7688202
X-RAY DIFFRACTIONf_dihedral_angle_d11.8962165
X-RAY DIFFRACTIONf_chiral_restr0.054923
X-RAY DIFFRACTIONf_plane_restr0.0021052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.254-2.2970.371650.33182533X-RAY DIFFRACTION99
2.297-2.34390.31191520.29142542X-RAY DIFFRACTION100
2.3439-2.39480.33051340.29252534X-RAY DIFFRACTION100
2.3948-2.45050.35031150.292605X-RAY DIFFRACTION100
2.4505-2.51180.32271180.27082584X-RAY DIFFRACTION100
2.5118-2.57970.31421250.26352590X-RAY DIFFRACTION100
2.5797-2.65560.31361450.24632546X-RAY DIFFRACTION100
2.6556-2.74120.28971420.24622560X-RAY DIFFRACTION100
2.7412-2.83920.25971540.2132539X-RAY DIFFRACTION100
2.8392-2.95280.22381270.1962602X-RAY DIFFRACTION100
2.9528-3.08710.20521060.19462584X-RAY DIFFRACTION100
3.0871-3.24980.22831380.192584X-RAY DIFFRACTION100
3.2498-3.45320.191440.20072584X-RAY DIFFRACTION100
3.4532-3.71960.24711240.19242597X-RAY DIFFRACTION100
3.7196-4.09350.20381520.17792578X-RAY DIFFRACTION100
4.0935-4.68470.16891540.14282599X-RAY DIFFRACTION100
4.6847-5.89810.20431410.16482636X-RAY DIFFRACTION100
5.8981-36.17380.2041440.19572700X-RAY DIFFRACTION98
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)
11.0496-0.0048-0.33564.56951.83545.12180.05880.0223-0.07160.113-0.08550.05810.3519-0.0267-0.00870.14450.0077-0.0110.24030.02220.257636.4222-12.881247.8456
27.1585-0.7740.64745.02190.80286.020.20930.86910.0555-0.66130.05050.08910.1505-0.107-0.27740.45470.0078-0.03540.40560.01860.345240.5238-25.180917.3591
36.24831.0849-2.96777.6661-0.86163.763-0.2084-1.79030.06650.5844-0.5876-0.3956-0.19330.68580.50120.9051-0.0404-0.07310.6786-0.03910.382547.35958.462487.0715
42.20710.6158-0.42711.37331.12334.94220.08190.00780.65320.63780.0394-0.5754-0.79060.7327-0.14790.611-0.2153-0.06820.4112-0.00030.40150.581816.949466.9923
52.35740.9626-2.29676.6561-3.08575.43210.2987-0.60510.50040.7163-0.3911-0.3994-1.72110.78580.04810.9582-0.1877-0.20760.4846-0.07890.455947.826119.674375.8972
61.8-0.35470.98284.6564-2.03575.6431-0.4065-0.40450.39850.14210.37640.2746-0.7606-0.37820.18020.70540.0359-0.02420.3896-0.04860.288339.199110.537481.3829
72.32740.80010.52535.70950.65224.845-0.0857-0.38930.33761.20190.00130.0364-0.7245-0.10380.12240.5635-0.05680.00960.2782-0.01910.327539.397312.918272.2206
87.8263-0.20822.06937.7960.60968.8098-0.1635-0.2980.26240.3061-0.13380.47520.1818-0.55780.17750.42250.02170.02130.31780.01180.251637.79691.941770.8988
92.94580.13250.0546.9048-0.62825.3751-0.20510.38740.1026-0.12240.0248-0.6561-0.1020.4640.15010.2323-0.04840.00680.3555-0.01010.289846.81015.655261.5624
102.89775.11651.3722.07592.70130.74650.3128-0.2140.69940.6856-0.4486-0.6699-0.12590.8679-0.06620.4827-0.0934-0.18310.52540.00690.567652.37169.007970.8334
113.9007-0.0082.12252.4415-0.19584.5933-0.04330.27880.4609-0.2682-0.0945-0.1358-0.7410.23850.09970.41130.0180.05290.22690.04270.324336.378218.739839.3345
121.8046-0.95131.56893.0718-0.94345.17940.0081-0.07540.0191-0.0125-0.01690.223-0.2307-0.3410.01960.22390.01060.04310.23930.01430.324731.327210.342744.9776
136.4818-2.08920.45964.04261.3634.15281.09031.4754-0.9525-1.0067-0.99810.43070.5345-0.0684-0.01130.74890.3166-0.10780.6738-0.19770.655110.974414.724317.0963
145.2068-3.02461.84344.52120.87043.72671.52451.9666-0.7239-1.1788-1.5304-0.08520.40460.3544-0.17681.10560.69420.05651.1021-0.1890.731318.872613.129712.492
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 3:10)
4X-RAY DIFFRACTION4chain 'C' and (resseq 11:36)
5X-RAY DIFFRACTION5chain 'C' and (resseq 37:50)
6X-RAY DIFFRACTION6chain 'C' and (resseq 51:60)
7X-RAY DIFFRACTION7chain 'C' and (resseq 61:96)
8X-RAY DIFFRACTION8chain 'C' and (resseq 97:109)
9X-RAY DIFFRACTION9chain 'C' and (resseq 110:136)
10X-RAY DIFFRACTION10chain 'C' and (resseq 137:146)
11X-RAY DIFFRACTION11chain 'B' and (resseq 10:94)
12X-RAY DIFFRACTION12chain 'B' and (resseq 95:150)
13X-RAY DIFFRACTION13chain 'B' and (resseq 151:222)
14X-RAY DIFFRACTION14chain 'B' and (resseq 223:294)

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