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- PDB-1fv2: The Hc fragment of tetanus toxin complexed with an analogue of it... -

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Basic information

Entry
Database: PDB / ID: 1fv2
TitleThe Hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B
ComponentsTETANUS TOXIN HEAVY CHAIN
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) / symbiont-mediated suppression of host exocytosis / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis ...tentoxilysin / symbiont-mediated perturbation of host neurotransmitter secretion / Toxicity of tetanus toxin (tetX) / symbiont-mediated suppression of host exocytosis / protein transmembrane transporter activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / endocytic vesicle membrane / toxin activity / proteolysis / extracellular region / zinc ion binding / 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 C-terminal / Clostridium neurotoxin, receptor binding N-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 C-terminal / Clostridium neurotoxin, receptor binding N-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: 2.5 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: Version format compliance
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 / database_PDB_caveat / 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_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_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 / _pdbx_validate_chiral.auth_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TETANUS TOXIN HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7764
Polymers53,9981
Non-polymers1,7793
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.849, 52.172, 117.353
Angle α, β, γ (deg.)90.00, 99.55, 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


Mass: 53997.773 Da / Num. of mol.: 1 / 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, tentoxilysin
#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.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CEQ / ETHYL-TRIMETHYL-SILANE


Mass: 102.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14Si
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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
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: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 19104 / Num. obs: 19104 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.767 / Num. unique all: 1777 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 57886
Reflection shell
*PLUS
% possible obs: 99.4 % / Mean I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementResolution: 2.5→40 Å / SU B: 23.729 / SU ML: 0.534 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / σ(I): 0 / ESU R: 0.652 / ESU R Free: 0.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27626 583 3.1 %RANDOM
Rwork0.2237 ---
all0.22528 18502 --
obs0.22528 18502 99.4 %-
Displacement parametersBiso mean: 35.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-1.21 Å2
2--1.51 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 119 120 3887
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.021
X-RAY DIFFRACTIONp_angle_d0.05
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9171.5
X-RAY DIFFRACTIONp_mcangle_it1.6812
X-RAY DIFFRACTIONp_scbond_it2.2463
X-RAY DIFFRACTIONp_scangle_it3.5674.5
X-RAY DIFFRACTIONp_plane_restr0.0060.02
X-RAY DIFFRACTIONp_chiral_restr0.1350.2
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1560.5
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rwork: 0.329
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)
10.84730.3695-0.00691.04050.35021.1744-0.0245-0.00440.0036-0.00460.0421-0.0484-0.1460.062-0.01760.01570.01620.00310.06410.01010.029445.66611.341941.2873
21.01980.2306-0.05360.7470.51381.9533-0.01090.0829-0.0485-0.12370.0289-0.08110.0590.0089-0.01790.05620.0331-0.00360.0467-0.00260.000236.3936-11.303514.7595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A865 - 1110
2X-RAY DIFFRACTION2A1111 - 1315
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / σ(F): 0 / % reflection Rfree: 3.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.43

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