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- PDB-3bo8: The High Resolution Crystal Structure of HLA-A1 Complexed with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bo8 | ||||||
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Title | The High Resolution Crystal Structure of HLA-A1 Complexed with the MAGE-A1 Peptide | ||||||
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Function / homology | ![]() T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / negative regulation of Notch signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / negative regulation of Notch signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
![]() | ![]() Title: Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: ![]() Title: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA) ...Title: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3 Authors: Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1w72S S: Starting model for refinement |
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Similar 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: 31636.955 Da / Num. of mol.: 1 Fragment: Ectodomain, Alpha-1, Alpha-2, Alpha-3, UNP Residues 25-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
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#2: Protein | ![]() Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() | ||
#3: Protein/peptide | Mass: 976.964 Da / Num. of mol.: 1 / Fragment: UNP Residues 161-169 / Source method: obtained synthetically Details: solid phase synthesis; This sequence occurs naturally in humans. References: UniProt: P43355 | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.14 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 3350, 0.2M Sodium Fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 20, 2005 / Details: mirror |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→63.888 Å / Num. obs: 43828 / % possible obs: 97 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.248 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.82 / Num. measured all: 24361 / Num. unique all: 6163 / Rsym value: 0.351 / % possible all: 95 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 0.431 / Cor.coef. Fo:Fc: 0.528
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1W72 Resolution: 1.8→19.65 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.672 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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