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Yorodumi- PDB-1fv2: The Hc fragment of tetanus toxin complexed with an analogue of it... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fv2 | |||||||||
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Title | The Hc fragment of tetanus toxin complexed with an analogue of its ganglioside receptor GT1B | |||||||||
Components | TETANUS TOXIN HEAVY CHAIN | |||||||||
Keywords | TOXIN / 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 | |||||||||
Biological species | Clostridium tetani (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | |||||||||
Authors | Fotinou, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fv2.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fv2.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 1fv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fv2 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fv2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is monomer |
-Components
#1: Protein | 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 |
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#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 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-CEQ / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 31, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Resolution: 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
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Displacement parameters | Biso mean: 35.706 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rwork: 0.329 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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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 |