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- PDB-4lo8: HA70(D3)-HA17 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4lo8
TitleHA70(D3)-HA17
Components
  • HA-17
  • HA-70
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) / extracellular region
Similarity search - Function
Hemagglutinin component HA-17 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium botulinum HA-17 domain / Clostridium enterotoxin / Clostridium enterotoxin / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Hemagglutinin component HA-17 / Jelly Rolls - #1090 / Hemagglutinin component HA-70, C-terminal / Haemagglutinin 70 C-terminal domain / Clostridium botulinum HA-17 domain / Clostridium enterotoxin / Clostridium enterotoxin / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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-70
B: HA-17
C: HA-70
D: HA-17
E: HA-70
F: HA-17
G: HA-70
H: HA-17


Theoretical massNumber of molelcules
Total (without water)183,6648
Polymers183,6648
Non-polymers00
Water7,440413
1
A: HA-70
B: HA-17


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-6 kcal/mol
Surface area17780 Å2
MethodPISA
2
C: HA-70
D: HA-17


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-5 kcal/mol
Surface area17810 Å2
MethodPISA
3
E: HA-70
F: HA-17


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-6 kcal/mol
Surface area17670 Å2
MethodPISA
4
G: HA-70
H: HA-17


Theoretical massNumber of molelcules
Total (without water)45,9162
Polymers45,9162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-5 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.810, 228.859, 78.718
Angle α, β, γ (deg.)90.00, 92.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28846.920 Da / Num. of mol.: 4 / Fragment: UNP residues 378-626
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-17 / HA-17 protein / HA17 / Ha17 protein / Non-toxin haemagglutinin HA17


Mass: 17069.195 Da / Num. of mol.: 4
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


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 4.8
Details: 0.1 M sodium acetate, 12% PEG2000 MME, 0.1 M cesium chloride, pH 4.8, EVAPORATION, temperature 292.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 62666 / Num. obs: 62548 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.7 / % possible all: 99

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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: 2.4→45.781 Å / SU ML: 0.72 / σ(F): 1.36 / Phase error: 28.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 3176 5.08 %RANDOM
Rwork0.1968 ---
obs0.1995 62548 99.37 %-
all-62666 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.63 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-18.7097 Å2-0 Å2-0.5295 Å2
2---12.2326 Å2-0 Å2
3----6.4771 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12267 0 0 413 12680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312523
X-RAY DIFFRACTIONf_angle_d0.7617036
X-RAY DIFFRACTIONf_dihedral_angle_d14.0164588
X-RAY DIFFRACTIONf_chiral_restr0.0551907
X-RAY DIFFRACTIONf_plane_restr0.0032214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43590.34211330.27972559X-RAY DIFFRACTION98
2.4359-2.47390.35381140.27212557X-RAY DIFFRACTION99
2.4739-2.51450.30551660.26922539X-RAY DIFFRACTION99
2.5145-2.55780.36341390.27012600X-RAY DIFFRACTION99
2.5578-2.60430.38181210.27232531X-RAY DIFFRACTION99
2.6043-2.65440.30991170.26292618X-RAY DIFFRACTION99
2.6544-2.70860.30181300.25222613X-RAY DIFFRACTION99
2.7086-2.76750.29731450.23812525X-RAY DIFFRACTION99
2.7675-2.83180.28551540.22982575X-RAY DIFFRACTION99
2.8318-2.90270.26131310.22212614X-RAY DIFFRACTION99
2.9027-2.98110.291270.21762568X-RAY DIFFRACTION99
2.9811-3.06880.26561190.20882629X-RAY DIFFRACTION99
3.0688-3.16790.27541390.20992547X-RAY DIFFRACTION100
3.1679-3.28110.2541640.19492607X-RAY DIFFRACTION99
3.2811-3.41240.24031380.19862553X-RAY DIFFRACTION99
3.4124-3.56760.24031440.18032594X-RAY DIFFRACTION100
3.5676-3.75560.20571380.18342582X-RAY DIFFRACTION99
3.7556-3.99080.23061310.17322572X-RAY DIFFRACTION100
3.9908-4.29870.21461420.16852599X-RAY DIFFRACTION100
4.2987-4.73090.21071450.14152608X-RAY DIFFRACTION100
4.7309-5.41460.19081570.14952564X-RAY DIFFRACTION100
5.4146-6.81820.25661370.20292615X-RAY DIFFRACTION100
6.8182-45.7890.21981450.18482603X-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)
14.40860.01990.23114.70670.08223.5944-0.17040.3371-0.4665-0.2511-0.1339-0.64890.35270.59590.22940.28010.04830.07770.32950.07140.371815.6906-58.40529.0647
22.80310.43390.60334.0130.51581.8049-0.14580.04840.089-0.0998-0.01430.2144-0.1284-0.13720.12160.1014-0.0011-0.02820.2348-0.00120.1684-2.932-43.286129.8059
33.9545-1.2153-0.47696.7629-0.80931.14670.25130.1829-0.0778-0.3053-0.0677-0.866-0.03250.1591-0.19930.4774-0.0287-0.09150.2217-0.07990.328821.7065-21.157632.2547
43.1642-0.1887-0.38223.75030.97731.77550.2286-0.0738-0.25920.1542-0.0868-0.14060.00380.18-0.1220.4467-0.0466-0.15310.18850.00150.288816.874-20.866241.3934
52.85360.93091.58885.10623.51942.7304-0.68340.1585-0.8747-0.8280.64860.07150.8339-0.76470.22051.9487-0.52670.15491.0873-0.03840.7059-16.5036-81.670752.8153
62.9115-0.87580.25778.32811.01552.1751-0.14590.4736-0.8746-1.66150.1060.17010.3531-0.29470.01291.1822-0.09610.06420.2743-0.03270.5721-12.5695-81.247663.6834
70.753-1.32941.06093.4642-1.28312.1087-0.08090.6657-0.2901-0.04520.2055-0.00030.0767-1.5835-0.01011.81860.3387-0.262-0.6757-0.53020.9162-16.5938-82.004959.1292
83.63410.3884-0.5584.87441.86225.4984-0.00740.3751-0.4999-0.6787-0.1961-0.12590.1575-0.26850.15570.5635-0.03340.08980.22470.04510.3872-14.1871-69.866670.9906
92.44971.0927-0.09362.3616-0.82732.38430.2-0.4833-0.36120.8353-0.1954-0.01140.1695-0.217-0.00140.6639-0.04930.08630.33750.07170.2731-12.7367-66.692781.3466
102.6692-1.0484-0.45073.22490.36924.5092-0.02010.2087-0.0216-0.1777-0.00710.1861-0.3665-0.39140.03160.55770.01210.06040.23380.02380.2043-11.5008-43.155958.3312
111.35140.35770.06522.00160.48614.11990.03760.06270.0220.17780.0821-0.1322-0.40070.0603-0.13380.581-0.00050.04260.1989-0.00660.1967-2.4214-42.659463.3392
124.72310.63470.44928.48247.05919.11120.0814-0.74540.3397-0.33370.0699-0.6217-0.11560.4553-0.20430.712-0.14870.0880.88960.09791.118720.41068.777887.5123
130.5236-0.4906-1.1570.46421.07952.48660.1234-0.88390.35310.7093-0.85480.0401-0.2854-0.05830.61970.9825-0.2894-0.36081.0331-0.09311.18420.82833.396196.3443
142.6811.0424-1.35955.77730.22222.46790.10580.0140.51710.2546-0.1886-0.7192-1.14320.7320.08890.55-0.1138-0.08310.29980.03840.594510.79466.965487.9204
153.23460.4207-0.28931.29271.18371.199-0.0362-0.70391.02120.8633-0.0976-0.4369-0.85640.98490.17940.7275-0.1611-0.20220.41030.06030.741210.89093.316793.0116
168.74415.0305-1.66375.64782.21924.0371-0.25910.7454-0.2442-1.13090.1615-0.4059-0.01180.38110.18350.59190.01750.05070.24290.09330.34219.7169-4.28981.9143
172.64040.3004-0.14894.9154-0.26572.9455-0.002-0.13410.34580.15670.15770.3692-0.0643-0.1389-0.10750.25130.0480.04030.250.01580.2133-4.8387-10.200792.5907
186.2085-2.0509-2.48514.12061.21313.6878-0.46950.44060.0403-0.86990.22110.71630.3722-0.49490.19250.7166-0.04-0.18510.26460.07430.4448-7.6886-10.556484.9579
193.7167-1.5762-1.1392.430.12882.8508-0.032-0.03460.28360.25480.36640.7385-0.243-0.508-0.18170.05410.05020.12010.30840.07210.4807-8.8564-8.644993.4054
203.99831.6836-0.73043.9206-2.13783.30160.0372-0.362-0.01970.4507-0.059-0.54710.03890.37760.01790.50760.09250.02370.3235-0.03950.141516.9832-32.374986.4187
213.14811.23741.03751.26550.43166.2365-0.16680.2837-0.4118-0.40420.3492-0.38860.4180.7845-0.11180.66310.18920.04180.3943-0.01370.310121.7742-36.912676.6423
222.3901-0.80640.19611.75360.36511.2623-0.0211-0.10170.1024-0.0898-0.0188-0.3947-0.09940.47260.02460.53890.05110.09850.26950.0080.25215.3166-28.006578.6334
232.9209-0.44740.43942.58010.88272.4007-0.09170.03410.0321-0.808-0.12910.07350.33620.21410.10210.82440.03410.05910.15030.01170.12516.6189-33.119277.4456
242.4647-4.1021-3.28587.30875.56514.36-0.8836-0.76360.11251.20280.81160.7022-0.2708-0.76270.42371.80140.06030.03350.9177-0.07580.7007-13.212328.857264.0767
255.3035-1.3562-0.46066.26873.34083.5052-0.1352-0.99550.6831.40410.1819-0.01190.3281-0.0047-0.0181.7639-0.09050.0433-0.4811-0.31580.4495-8.367125.056557.2088
262.6373-0.47641.55562.10810.37031.605-0.5432-0.25360.76210.6025-0.11340.8574-0.273-0.18470.42041.04670.0554-0.09310.0212-0.11150.7906-10.578530.120150.0887
270.43670.0944-1.21544.6628-0.35783.5906-0.3624-0.71310.39280.57140.16080.8076-0.2265-0.9820.1121.33730.03790.1568-0.0506-0.30181.0073-13.531528.783257.6811
282.849-0.94380.36074.03850.87473.70610.10610.0367-0.13110.67060.0266-0.1493-0.0403-0.0679-0.18030.88920.0422-0.12210.23790.03620.5156-7.583816.089549.233
292.0979-0.85410.11935.4074-1.13451.28460.20760.20320.1446-1.0306-0.21121.2046-0.4525-0.2231-0.01170.79540.0168-0.23130.28840.01840.3112-13.119312.249736.9778
301.9687-0.5760.58553.008-1.82912.63-0.10830.36390.2773-1.06240.05460.1326-0.6038-0.27430.03060.9050.0365-0.19030.24690.05650.269-8.094812.815936.3422
313.14720.97530.21414.92181.33424.57220.0641-0.512-0.14920.51050.06820.06350.1869-0.2088-0.09540.5688-0.0577-0.05120.30890.0560.2294-6.2497-9.493560.8847
322.9045-0.9851-0.15961.65180.60383.13930.0006-0.2352-0.33720.17110.1516-0.04440.09650.0897-0.14360.5261-0.0762-0.10440.21390.02340.23992.8034-10.01955.7677
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 380:507)
2X-RAY DIFFRACTION2chain 'A' and (resseq 508:626)
3X-RAY DIFFRACTION3chain 'B' and (resseq 4:60)
4X-RAY DIFFRACTION4chain 'B' and (resseq 61:146)
5X-RAY DIFFRACTION5chain 'C' and (resseq 380:405)
6X-RAY DIFFRACTION6chain 'C' and (resseq 406:474)
7X-RAY DIFFRACTION7chain 'C' and (resseq 475:493)
8X-RAY DIFFRACTION8chain 'C' and (resseq 494:529)
9X-RAY DIFFRACTION9chain 'C' and (resseq 530:626)
10X-RAY DIFFRACTION10chain 'D' and (resseq 4:60)
11X-RAY DIFFRACTION11chain 'D' and (resseq 61:146)
12X-RAY DIFFRACTION12chain 'E' and (resseq 380:391)
13X-RAY DIFFRACTION13chain 'E' and (resseq 392:405)
14X-RAY DIFFRACTION14chain 'E' and (resseq 406:460)
15X-RAY DIFFRACTION15chain 'E' and (resseq 461:493)
16X-RAY DIFFRACTION16chain 'E' and (resseq 494:507)
17X-RAY DIFFRACTION17chain 'E' and (resseq 508:574)
18X-RAY DIFFRACTION18chain 'E' and (resseq 575:594)
19X-RAY DIFFRACTION19chain 'E' and (resseq 595:626)
20X-RAY DIFFRACTION20chain 'F' and (resseq 5:60)
21X-RAY DIFFRACTION21chain 'F' and (resseq 61:75)
22X-RAY DIFFRACTION22chain 'F' and (resseq 76:101)
23X-RAY DIFFRACTION23chain 'F' and (resseq 102:146)
24X-RAY DIFFRACTION24chain 'G' and (resseq 380:405)
25X-RAY DIFFRACTION25chain 'G' and (resseq 406:428)
26X-RAY DIFFRACTION26chain 'G' and (resseq 429:474)
27X-RAY DIFFRACTION27chain 'G' and (resseq 475:493)
28X-RAY DIFFRACTION28chain 'G' and (resseq 494:521)
29X-RAY DIFFRACTION29chain 'G' and (resseq 522:562)
30X-RAY DIFFRACTION30chain 'G' and (resseq 563:626)
31X-RAY DIFFRACTION31chain 'H' and (resseq 4:60)
32X-RAY DIFFRACTION32chain 'H' and (resseq 61:146)

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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