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Yorodumi- PDB-1a3r: FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a3r | ||||||
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Title | FAB FRAGMENT (ANTIBODY 8F5) COMPLEXED WITH PEPTIDE FROM HUMAN RHINOVIRUS (SEROTYPE 2) VIRAL CAPSID PROTEIN VP2 (RESIDUES 156-170) | ||||||
Components |
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Keywords | Viral protein/Immune system / IMMUNOGLOBULIN / ANTIBODY / RHINOVIRUS / NEUTRALIZATION / CONTINUOUS EPITOPE / COMPLEX (IMMUNOGLOBULIN-VIRAL PEPTIDE) / Viral protein-Immune system COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / complement activation, classical pathway / T=pseudo3 icosahedral viral capsid / antigen binding / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / antibacterial humoral response / DNA replication / blood microparticle / RNA helicase activity / induction by virus of host autophagy / immune response / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / extracellular space / extracellular exosome / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Human rhinovirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tormo, J. / Blaas, D. / Fita, I. | ||||||
Citation | Journal: EMBO J. / Year: 1994 Title: Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. Authors: Tormo, J. / Blaas, D. / Parry, N.R. / Rowlands, D. / Stuart, D. / Fita, I. #1: Journal: Protein Sci. / Year: 1992 Title: Three-Dimensional Structure of the Fab Fragment of a Neutralizing Antibody to Human Rhinovirus Serotype 2 Authors: Tormo, J. / Stadler, E. / Skern, T. / Auer, H. / Kanzler, O. / Betzel, C. / Blaas, D. / Fita, I. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Fab Fragment of a Neutralizing Monoclonal Antibody Directed Against Human Rhinovirus Serotype 2 Authors: Tormo, J. / Fita, I. / Kanzler, O. / Blaas, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3r.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3r.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 1a3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3r_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
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Full document | 1a3r_full_validation.pdf.gz | 423.8 KB | Display | |
Data in XML | 1a3r_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1a3r_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3r ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3r | HTTPS FTP |
-Related structure data
Related structure data | 1bbdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24416.984 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT (PAPAIN DIGESTION) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L64*PLUS |
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#2: Antibody | Mass: 23588.201 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT (PAPAIN DIGESTION) / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q505N9*PLUS |
#3: Protein/peptide | Mass: 1710.905 Da / Num. of mol.: 1 / Fragment: RESIDUES 156 - 170 / Source method: isolated from a natural source / Details: COMMON COLD VIRUS / Source: (natural) Human rhinovirus 2 / Genus: Rhinovirus / Species: Human rhinovirus A / Strain: SEROTYPE 2 / References: UniProt: P04936 |
#4: Water | ChemComp-HOH / |
Compound details | NH2: THE SYNTHETIC PEPTIDE HAS ITS C-TERMINAL END BLOCKED WITH AN AMIDE GROUP. |
Sequence details | THE PEPTIDE IS NUMBERED ACCORDING TO THE VIENNA ISOLATE SEQUENCE (SKERN ET AL., NUCLEIC ACIDS RES., ...THE PEPTIDE IS NUMBERED ACCORDING TO THE VIENNA ISOLATE SEQUENCE (SKERN ET AL., NUCLEIC ACIDS RES., 13:2111- 2126(1985) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: FAB-PEPTIDE COMPLEX WAS CRYSTALLIZED FROM 0.9 M SODIUM CITRATE, 25 MM SODIUM CHLORIDE, 50 MM TRIS-HCL, PH 7.75, pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 1991 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 28392 / % possible obs: 94.6 % / Biso Wilson estimate: 13.6 Å2 / Rsym value: 0.062 |
Reflection shell | Resolution: 2.1→2.15 Å / Rsym value: 0.18 / % possible all: 90.2 |
Reflection | *PLUS Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BBD Resolution: 2.1→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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