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Yorodumi- PDB-1ejo: FAB FRAGMENT OF NEUTRALISING MONOCLONAL ANTIBODY 4C4 COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ejo | ||||||
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Title | FAB FRAGMENT OF NEUTRALISING MONOCLONAL ANTIBODY 4C4 COMPLEXED WITH G-H LOOP FROM FMDV. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FMDV / antigenic-antibody interactions / RGD motif / G-H loop of VP1. | ||||||
Function / homology | Function and homology information L-peptidase / modulation by virus of host chromatin organization / immunoglobulin complex / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation ...L-peptidase / modulation by virus of host chromatin organization / immunoglobulin complex / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / adaptive immune response / viral protein processing / immune response / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / extracellular space / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Ochoa, W.F. / Kalko, S.G. / Gomes, P. / Fita, I. / Verdaguer, N. | ||||||
Citation | Journal: J.Gen.Virol. / Year: 2000 Title: A multiply substituted G-H loop from foot-and-mouth disease virus in complex with a neutralizing antibody: a role for water molecules. Authors: Ochoa, W.F. / Kalko, S.G. / Mateu, M.G. / Gomes, P. / Andreu, D. / Domingo, E. / Fita, I. / Verdaguer, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ejo.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ejo.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ejo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/1ejo ftp://data.pdbj.org/pub/pdb/validation_reports/ej/1ejo | 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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-Components
#1: Antibody | Mass: 23755.156 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01660*PLUS |
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#2: Antibody | Mass: 23572.383 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PF95*PLUS |
#3: Protein/peptide | Mass: 1625.736 Da / Num. of mol.: 1 / Fragment: G-H LOOP / Source method: obtained synthetically Details: This synthetic peptide corresponds to the sequence of the G-H loop from foot-and-mouth disease virus. References: GenBank: 210410, UniProt: P15072*PLUS |
#4: 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: 2.5 Å3/Da / Density % sol: 50.77 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 4K 16%, LiCl 0.2 M, Tris HCl 50mM , pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 26286 / Num. obs: 24105 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.093 / Net I/σ(I): 4.86 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 96.7 % / Rmerge(I) obs: 0.24 / Num. unique all: 1232 / % possible all: 96.7 |
Reflection shell | *PLUS % possible obs: 96.7 % |
-Processing
Software |
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Refinement | Resolution: 2.3→15 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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