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- PDB-4lo0: Apo HA17-HA33 -

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Basic information

Entry
Database: PDB / ID: 4lo0
TitleApo HA17-HA33
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
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.055 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 1.2Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)85,2333
Polymers85,2333
Non-polymers00
Water5,098283
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-24 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.599, 118.680, 162.509
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-265-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
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: Jul 3, 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: 2.055→47.9 Å / Num. all: 62951 / Num. obs: 62896 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.7
Reflection shellResolution: 2.055→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2 / % possible all: 97.5

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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: 2.055→35.636 Å / SU ML: 0.67 / σ(F): 1.35 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 3172 5.04 %RANDOM
Rwork0.1879 ---
obs0.1893 62896 97.87 %-
all-62951 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.719 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.8294 Å2-0 Å2-0 Å2
2---8.632 Å2-0 Å2
3----5.1974 Å2
Refinement stepCycle: LAST / Resolution: 2.055→35.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 0 283 6128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015985
X-RAY DIFFRACTIONf_angle_d1.2148168
X-RAY DIFFRACTIONf_dihedral_angle_d14.6942151
X-RAY DIFFRACTIONf_chiral_restr0.089913
X-RAY DIFFRACTIONf_plane_restr0.0051052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.055-2.08570.36481280.3162499X-RAY DIFFRACTION96
2.0857-2.11830.31181230.30142572X-RAY DIFFRACTION98
2.1183-2.1530.31621330.28142600X-RAY DIFFRACTION98
2.153-2.19010.33481340.2692543X-RAY DIFFRACTION98
2.1901-2.22990.29281400.23662562X-RAY DIFFRACTION98
2.2299-2.27280.261500.23722569X-RAY DIFFRACTION98
2.2728-2.31920.26041370.22442568X-RAY DIFFRACTION98
2.3192-2.36960.30581440.2252585X-RAY DIFFRACTION98
2.3696-2.42470.28311490.22482585X-RAY DIFFRACTION98
2.4247-2.48540.29651420.22662585X-RAY DIFFRACTION98
2.4854-2.55250.25471380.21522583X-RAY DIFFRACTION98
2.5525-2.62760.26071300.20282586X-RAY DIFFRACTION98
2.6276-2.71240.25071230.20462637X-RAY DIFFRACTION98
2.7124-2.80930.23381340.20162604X-RAY DIFFRACTION99
2.8093-2.92170.19951310.18352609X-RAY DIFFRACTION99
2.9217-3.05460.21711320.18452626X-RAY DIFFRACTION98
3.0546-3.21560.241430.18752612X-RAY DIFFRACTION99
3.2156-3.41690.2081400.19362625X-RAY DIFFRACTION99
3.4169-3.68050.21881420.18062624X-RAY DIFFRACTION98
3.6805-4.05040.18781510.16692598X-RAY DIFFRACTION98
4.0504-4.63540.15131510.13282627X-RAY DIFFRACTION97
4.6354-5.8360.17431440.1492615X-RAY DIFFRACTION97
5.836-35.6410.19861330.1952710X-RAY DIFFRACTION96
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)
10.87650.0417-0.25093.971.82224.48490.02030.0245-0.08220.1397-0.04780.07220.3007-0.00690.01980.1360.002-0.00550.21350.01640.234736.2506-12.897747.8889
26.4356-0.96040.07084.84850.61665.92950.21040.84590.0393-0.6693-0.00190.11360.1132-0.0942-0.21290.38360.0156-0.03460.35820.01560.270240.4289-25.183817.395
32.51540.8793-0.83962.8844-0.42281.0271-0.2541-0.53120.18560.6794-0.1609-0.1033-0.27290.75560.21620.7611-0.1396-0.12050.4513-0.03550.328549.302211.535581.4191
44.5152-0.3805-0.6016.08950.46814.4410.04180.00140.77710.37130.2232-0.5967-0.9340.4601-0.23950.5775-0.182-0.04360.36350.00420.320949.932717.493964.1856
53.60213.2189-2.30477.5525-3.74643.55870.2888-0.71320.53610.2394-0.3024-0.2006-1.07320.67050.0711.0156-0.1786-0.21610.3768-0.09710.444347.736619.619575.9079
62.58060.5770.46935.1514-3.46377.0632-0.2237-0.48110.2008-0.06590.08210.3216-0.3809-0.01770.16410.6374-0.0001-0.01120.3219-0.04790.21539.04910.521881.3892
72.78461.57880.93174.12282.29433.501-0.1549-0.34570.61880.6363-0.12990.382-1.1781-0.08040.25580.6366-0.01830.00480.22-0.03480.38936.761217.592269.5097
83.5901-0.11960.49674.8180.85034.7973-0.0821-0.41840.27830.91930.09470.1421-0.5368-0.16540.08930.5821-0.0310.03750.3113-0.02220.290738.862510.064974.0063
92.59660.01640.19886.4296-0.41885.0718-0.14650.06870.03680.36030.0076-0.3289-0.14780.26160.13450.2276-0.0152-0.03350.2491-0.01470.225544.50764.522865.2821
104.20196.35663.76119.66665.72773.37610.0928-0.17050.40420.93350.0103-0.5840.05970.7679-0.21880.431-0.0754-0.1740.4874-0.01880.424752.20298.958970.8724
112.4458-0.78311.2452.7276-0.60373.72070.04440.14930.1372-0.2062-0.080.0133-0.47850.010.03440.29120.02320.0420.18880.01770.261534.278615.394341.5803
128.0755-2.11751.49844.03521.04694.01811.09561.3525-0.8869-0.9089-0.83390.52740.4909-0.1274-0.21290.59010.2546-0.12880.625-0.13620.539710.845415.541918.2042
134.3377-3.28920.86043.80351.36433.61881.08191.9044-0.5951-1.307-0.62250.01650.48150.5006-0.36631.14420.6252-0.04021.13-0.21520.681718.463912.581411.9573
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 61:75)
8X-RAY DIFFRACTION8chain 'C' and (resseq 76:93)
9X-RAY DIFFRACTION9chain 'C' and (resseq 94:136)
10X-RAY DIFFRACTION10chain 'C' and (resseq 137:146)
11X-RAY DIFFRACTION11chain 'B' and (resseq 10:150)
12X-RAY DIFFRACTION12chain 'B' and (resseq 151:216)
13X-RAY DIFFRACTION13chain 'B' and (resseq 217:294)

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