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- PDB-1fv3: THE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH AN ANALOGUE OF IT... -

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Basic information

Entry
Database: PDB / ID: 1fv3
TitleTHE HC FRAGMENT OF TETANUS TOXIN COMPLEXED WITH AN ANALOGUE OF ITS GANGLIOSIDE RECEPTOR GT1B
ComponentsTETANUS TOXIN HEAVY CHAINTetanospasmin
KeywordsTOXIN / carbohydrate / ganglioside / multi-valent binding / receptor
Function / homology
Function and homology information


tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / zinc ion binding / extracellular region / plasma membrane / cytosol
Similarity search - Function
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ETHYL-TRIMETHYL-SILANE / PHOSPHATE ION / Tetanus toxin
Similarity search - Component
Biological speciesClostridium tetani (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsFotinou, C. / Emsley, P. / Black, I. / Ando, H. / Ishida, H. / Kiso, M. / Sinha, K.A. / Fairweather, N.F. / Isaacs, N.W.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The crystal structure of tetanus toxin Hc fragment complexed with a synthetic GT1b analogue suggests cross-linking between ganglioside receptors and the toxin.
Authors: Fotinou, C. / Emsley, P. / Black, I. / Ando, H. / Ishida, H. / Kiso, M. / Sinha, K.A. / Fairweather, N.F. / Isaacs, N.W.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: The Structures of the HC Fragment of Tetanus Toxin with Carbohydrate Subunit Complexes Provide Insight into Ganglioside Binding
Authors: Emsley, P. / Fotinou, C. / Black, I. / Fairweather, N.F. / Charles, I.G. / Watts, C. / Hewitt, E. / Isaacs, N.W.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of the receptor binding fragment Hc of tetanus neurotoxin
Authors: Umland, T.C. / Wingert, L.M. / Swaminathan, S. / Furey, W.F. / Schmidt, J.J. / Sax, M.
History
DepositionSep 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jun 8, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TETANUS TOXIN HEAVY CHAIN
B: TETANUS TOXIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4587
Polymers107,9962
Non-polymers3,4625
Water4,342241
1
A: TETANUS TOXIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6813
Polymers53,9981
Non-polymers1,6842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TETANUS TOXIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7764
Polymers53,9981
Non-polymers1,7793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.311, 53.068, 118.278
Angle α, β, γ (deg.)90.00, 89.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is monomer

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Components

#1: Protein TETANUS TOXIN HEAVY CHAIN / Tetanospasmin


Mass: 53997.773 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN OF HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium tetani (bacteria) / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / References: UniProt: P04958
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1581.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-8DNeup5Acb2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2b_2-6_5*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-5-2-4/a4-b1_b3-c2_b4-e1_c8-d2_e3-f1_f3-g2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][b-D-Neup5Ac]{[(8+2)][a-D-Neup5Ac]{}}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CEQ / ETHYL-TRIMETHYL-SILANE


Mass: 102.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14Si
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe HIS TAG was not cleaved and it is not seen in the density.

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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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 20% Polyethylene glycol 8000, sodium-potassium phosphate, TRIS, imidazole, sodium chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.8 mg/mlprotein1drop
220 %PEG40001reservoir
30.2 Mimidazole-malate1reservoirpH7.0
40.1 MTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.782
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.782 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 49658 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 3.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.97 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 166764
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.3→30 Å / SU B: 17.184 / SU ML: 0.411 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.289 / Stereochemistry target values: ENGH & HUBER
Details: USE OF MAXIMUM LIKELILHOOD REFINEMENT (REFMAC REFINEMENT PROGRAMM)
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1543 3.1 %RANDOM
Rwork0.237 ---
obs0.239 48094 98.3 %-
all-48094 --
Displacement parametersBiso mean: 32.84 Å2
Baniso -1Baniso -2Baniso -3
1-4.91 Å20 Å2-2.3 Å2
2---1.74 Å20 Å2
3----3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7296 0 233 241 7770
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rwork: 0.334
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)
10.8581-0.29630.63881.0479-0.14791.8892-0.0894-0.0792-0.1360.0357-0.04050.02320.13890.03810.12990.06230.00890.01590.10560.05070.08918.7808-8.285246.5551
21.8706-0.40711.01141.2052-0.69972.1387-0.067-0.03840.0290.0244-0.02920.0639-0.2265-0.09440.09620.05090.0083-0.04780.069-0.00540.06273.51538.084319.3561
30.641-0.0711-0.15631.3820.32191.85070.0186-0.04420.08490.14170.0844-0.0894-0.20740.1305-0.1030.1176-0.00110.02320.0557-0.02250.059757.348241.725144.4922
40.5441-0.0793-0.33451.44340.88392.5470.0240.0007-0.0014-0.04270.0698-0.1338-0.00350.1579-0.09380.01660.00510.03280.0742-0.01290.072155.217320.363516.2413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A865 - 1110
2X-RAY DIFFRACTION2A1111 - 1315
3X-RAY DIFFRACTION3B865 - 1110
4X-RAY DIFFRACTION4B1111 - 1315
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.38

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