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Yorodumi- PDB-1fpt: THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN THE FAB FRAGME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fpt | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF THE COMPLEX BETWEEN THE FAB FRAGMENT OF AN NEUTRALIZING ANTIBODY FOR TYPE 1 POLIOVIRUS AND ITS VIRAL EPITOPE | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY/PV-1 FRAGMENT) / COMPLEX (ANTIBODY-PV-1 FRAGMENT) / COMPLEX (ANTIBODY-PV-1 FRAGMENT) complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding ...symbiont-mediated suppression of host translation initiation / positive regulation of B cell activation / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / immunoglobulin mediated immune response / antigen processing and presentation / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / multivesicular body / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / response to bacterium / endocytosis involved in viral entry into host cell / : / positive regulation of immune response / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / extracellular space / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Human poliovirus 1 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | Wien, M.W. / Hogle, J.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope. Authors: Wien, M.W. / Filman, D.J. / Stura, E.A. / Guillot, S. / Delpeyroux, F. / Crainic, R. / Hogle, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fpt.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fpt.ent.gz | 76.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fpt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/1fpt ftp://data.pdbj.org/pub/pdb/validation_reports/fp/1fpt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 4: ARG H 40 - PRO H 41 OMEGA = 247.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151 |
-Components
#1: Antibody | Mass: 1940.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human poliovirus 1 / Genus: Enterovirus / Species: Poliovirus / Strain: Mahoney / References: UniProt: P03299, UniProt: P03300*PLUS |
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#2: Antibody | Mass: 24080.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
#3: Antibody | Mass: 23478.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01865 |
#4: Water | ChemComp-HOH / |
Sequence details | THE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID- ...THE FAB FRAGMENT IS NUMBERED ACCORDING TO THE CONVENTION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.16 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 13342 / % possible obs: 86 % / Observed criterion σ(I): 15.6 / Num. measured all: 87269 / Rmerge(I) obs: 0.0986 |
-Processing
Software |
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Refinement | Resolution: 3→10 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15 Å2 |