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- PDB-1i8k: CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i8k | ||||||
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Title | CRYSTAL STRUCTURE OF DSFV MR1 IN COMPLEX WITH THE PEPTIDE ANTIGEN OF THE MUTANT EPIDERMAL GROWTH FACTOR RECEPTOR, EGFRVIII, AT LIQUID NITROGEN TEMPERATURE | ||||||
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![]() | IMMUNE SYSTEM / antibody-peptide complex / immunoglobulin fold / peptide antigen / type II' beta turn. | ||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Landry, R.C. / Klimowicz, A.C. / Lavictoire, S.J. / Borisova, S. / Kottachchi, D.T. / Lorimer, I.A. / Evans, S.V. | ||||||
![]() | ![]() Title: Antibody recognition of a conformational epitope in a peptide antigen: Fv-peptide complex of an antibody fragment specific for the mutant EGF receptor, EGFRvIII. Authors: Landry, R.C. / Klimowicz, A.C. / Lavictoire, S.J. / Borisova, S. / Kottachchi, D.T. / Lorimer, I.A. / Evans, S.V. | ||||||
History |
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Remark 999 | SEQUENCE Residues 100 of chain A and 344 of chain B have been mutated to Cys residues to introduce ...SEQUENCE Residues 100 of chain A and 344 of chain B have been mutated to Cys residues to introduce a disulfide bridge between chains A and B. There is no sequence database match for chain C because the sequence of EGFRvIII has not yet been deposited in any database. The DNA sequence of the normal EGF receptor has been deposited (NM_005228). |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.8 KB | Display | ![]() |
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PDB format | ![]() | 47.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.8 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11745.038 Da / Num. of mol.: 1 / Mutation: D100C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 13712.354 Da / Num. of mol.: 1 / Mutation: R344C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1421.531 Da / Num. of mol.: 1 / Fragment: N-TERMINAL FRAGMENT / Source method: obtained synthetically Details: The peptide sequence is from the N-terminal of the mutant epidermal growth factor receptor, EGFRvIII |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium chloride, MPD, PEG 10K, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 1999 |
Radiation | Monochromator: collimating mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→6 Å / Num. all: 25057 / Num. obs: 24309 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.26 % / Biso Wilson estimate: 13.94 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.94 % / Rmerge(I) obs: 0.143 / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 24641 / % possible obs: 98.5 % / Num. measured all: 25654 |
Reflection shell | *PLUS % possible obs: 95.7 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 13 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 6 Å / σ(F): 3 / Rfactor Rfree: 0.225 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13 Å2 | ||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.276 / Rfactor Rwork: 0.216 |