[English] 日本語
Yorodumi- PDB-1g7p: CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g7p | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF MHC CLASS I H-2KB HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND YEAST ALPHA-GLUCOSIDASE | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / MHC class I / H-2Kb / YEAST / S. cerevisiae / alpha-glucosidase | |||||||||
Function / homology | Function and homology information maltose catabolic process / alpha-glucosidase / : / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I ...maltose catabolic process / alpha-glucosidase / : / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to bacterium / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Apostolopoulos, V. / Yu, M. / Corper, A.L. / Li, W. / McKenzie, I.F. / Teyton, L. / Wilson, I.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal structure of a non-canonical high affinity peptide complexed with MHC class I: a novel use of alternative anchors. Authors: Apostolopoulos, V. / Yu, M. / Corper, A.L. / Li, W. / McKenzie, I.F. / Teyton, L. / Wilson, I.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g7p.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g7p.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 1g7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g7p_validation.pdf.gz | 863.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1g7p_full_validation.pdf.gz | 870.7 KB | Display | |
Data in XML | 1g7p_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1g7p_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g7p ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g7p | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 22-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 / References: UniProt: P01901 |
---|---|
#2: Protein | Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 / References: UniProt: P01887 |
-Protein/peptide / Non-polymers , 2 types, 282 molecules P
#3: Protein/peptide | Mass: 1089.208 Da / Num. of mol.: 1 / Fragment: RESIDUES 438-446 / Source method: obtained synthetically Details: The 9-residue peptide of ALPHA-GLUCOSIDASE P1 was chemically synthesized References: GenBank: 411229, UniProt: P07265*PLUS, alpha-glucosidase |
---|---|
#6: Water | ChemComp-HOH / |
-Sugars , 2 types, 2 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.15 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.25 Details: sodium/potassium phosphate, MPD, pH 7.25, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.025 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.025 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 89041 / Num. obs: 79109 / % possible obs: 88.8 % / Observed criterion σ(I): 2.06 / Redundancy: 3.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.467 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 82816 / % possible obs: 92.9 % |
Reflection shell | *PLUS % possible obs: 82.3 % / Num. unique obs: 3649 / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→23.38 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 712061.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.38 Å2 / ksol: 0.426 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→23.38 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.24 |