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Basic information

Entry
Database: PDB / ID: 4lo5
TitleHA70-alpha2,3-SiaLC
Components(HA-70) x 2
KeywordsPROTEIN TRANSPORT / progenitor toxin complex / botulinum neurotoxin / botulism / neurotoxin associated protein / hemagglutinin / carbohydrate/sugar binding / secreted protein
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Proaerolysin; Chain A, domain 3 - #20 / Proaerolysin; Chain A, domain 3 / Clostridium enterotoxin / Clostridium enterotoxin / Beta Complex / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
3'-sialyl-alpha-lactose / HA-70
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_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 / _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-70
B: HA-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7574
Polymers71,0882
Non-polymers6692
Water2,018112
1
A: HA-70
B: HA-70
hetero molecules

A: HA-70
B: HA-70
hetero molecules

A: HA-70
B: HA-70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,27112
Polymers213,2646
Non-polymers2,0076
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area24390 Å2
ΔGint-105 kcal/mol
Surface area74640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)260.740, 260.740, 260.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein HA-70 / HA70 / Non-toxin haemagglutinin HA70


Mass: 21939.703 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KHU9
#2: Protein HA-70 / HA70 / Non-toxin haemagglutinin HA70


Mass: 49148.324 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha70 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KHU9
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFULL-LENGTH HA70 WAS CLEAVED INTO CHAIN A (UNP RESIDUES 2-189) AND CHAIN B (UNP RESIDUES 206-626). ...FULL-LENGTH HA70 WAS CLEAVED INTO CHAIN A (UNP RESIDUES 2-189) AND CHAIN B (UNP RESIDUES 206-626). THE EXACT CLEAVAGE POINT ON THE TKNIPTNNIFNSKVSS LINKING SEQUENCE IS NOT KNOWN.

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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: 5.19 Å3/Da / Density % sol: 76.3 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 4.4
Details: 0.1 M sodium acetate, 1.5 M ammonium chloride, pH 4.4, EVAPORATION, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2012
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.7→47.6 Å / Num. all: 41471 / Num. obs: 41439 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.717 Å / SU ML: 0.71 / σ(F): 0 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2082 5.02 %RANDOM
Rwork0.1897 ---
all0.1906 41471 --
obs0.1906 41439 99.82 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.35 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3791 Å20 Å20 Å2
2--2.3791 Å20 Å2
3---2.3791 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 44 112 4916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034900
X-RAY DIFFRACTIONf_angle_d0.7976668
X-RAY DIFFRACTIONf_dihedral_angle_d15.2771826
X-RAY DIFFRACTIONf_chiral_restr0.054755
X-RAY DIFFRACTIONf_plane_restr0.003869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76310.35441290.31792611X-RAY DIFFRACTION100
2.7631-2.83220.39931460.30992557X-RAY DIFFRACTION100
2.8322-2.90870.29491450.27832582X-RAY DIFFRACTION100
2.9087-2.99430.24481210.26412605X-RAY DIFFRACTION100
2.9943-3.09090.3111510.23312573X-RAY DIFFRACTION100
3.0909-3.20140.24781450.22392591X-RAY DIFFRACTION100
3.2014-3.32950.24331490.20782591X-RAY DIFFRACTION100
3.3295-3.4810.21131330.21182595X-RAY DIFFRACTION100
3.481-3.66440.23431320.19552631X-RAY DIFFRACTION100
3.6644-3.89390.20321150.18352656X-RAY DIFFRACTION100
3.8939-4.19430.16841380.15762609X-RAY DIFFRACTION100
4.1943-4.6160.1441520.13332624X-RAY DIFFRACTION100
4.616-5.28310.14551400.13382659X-RAY DIFFRACTION100
5.2831-6.65260.21641430.19982688X-RAY DIFFRACTION100
6.6526-44.72270.20171430.19022785X-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)
18.2435-4.1466.44836.6338-1.9785.46470.28380.0804-1.26570.03510.0931-0.92071.23750.0424-0.05760.93020.32780.45770.76380.08241.017623.1854-37.17819.5491
23.3498-2.22640.63613.8351-1.8093.2077-0.2302-0.0238-0.21570.34660.02060.03490.0420.22020.23520.52320.0590.08990.33290.06980.4189-0.0801-16.93659.9364
35.7776-2.38851.82847.8822-3.26242.0605-0.1086-1.30390.0110.2079-0.1585-0.7103-0.22360.65910.44030.52690.00160.13760.740.11360.683622.9248-22.53215.4928
43.3202-0.18344.30974.82-3.63287.97-0.86940.2908-0.3048-0.1361-0.6648-1.1857-0.54980.52831.22730.76570.04060.11570.88350.15460.684917.9461-12.92315.565
55.72146.2714.64227.81533.83565.3437-0.4208-0.26820.3897-0.5015-0.16180.41870.3033-0.64890.44290.58790.0710.0890.55990.10130.5757-10.2895-16.27731.216
68.5259-3.3431.41492.7297-0.58772.335-0.3211-0.062-0.16430.17270.23480.08520.39880.2099-0.10750.63770.18470.17810.47050.15990.50669.1327-27.360111.1773
73.7735-0.07463.27733.5319-3.45166.22440.4215-0.7771-0.5237-0.2433-0.02260.03010.36550.22970.11180.52330.20760.27430.64950.29240.724217.3931-28.726615.0581
85.75682.0625-1.50155.3379-1.18634.6348-0.20880.2953-1.3448-0.2298-0.16030.31640.9151-0.58060.29370.65940.06370.140.4550.11790.7338-11.3775-24.950411.1579
97.1821-2.844-3.25333.20510.33934.15040.27060.0863-0.666-0.4179-0.4042-0.14740.31010.50080.12430.67520.23580.21580.49260.08660.649514.7233-30.61288.775
100.9181-0.44241.05071.8124-1.8143.1786-0.05520.09650.04920.17750.07250.1561-0.2028-0.1878-0.02130.47010.05820.17480.35070.08320.5179-12.6998-11.89420.6745
113.25120.1148-0.88123.553-0.90912.12810.1306-0.0319-0.2551-0.0079-0.3544-0.24570.09780.26510.21670.50770.09650.05650.27740.04010.4734-1.6194-44.759641.249
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 20:33)
2X-RAY DIFFRACTION2chain 'A' and (resseq 34:71)
3X-RAY DIFFRACTION3chain 'A' and (resseq 72:91)
4X-RAY DIFFRACTION4chain 'A' and (resseq 92:102)
5X-RAY DIFFRACTION5chain 'A' and (resseq 103:115)
6X-RAY DIFFRACTION6chain 'A' and (resseq 116:137)
7X-RAY DIFFRACTION7chain 'A' and (resseq 138:147)
8X-RAY DIFFRACTION8chain 'A' and (resseq 148:168)
9X-RAY DIFFRACTION9chain 'A' and (resseq 169:189)
10X-RAY DIFFRACTION10chain 'B' and (resseq 206:384)
11X-RAY DIFFRACTION11chain 'B' and (resseq 385:626)

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