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Yorodumi- PDB-1ed3: CRYSTAL STRUCTURE OF RAT MINOR HISTOCOMPATIBILITY ANTIGEN COMPLEX... -
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-Basic information
Entry | Database: PDB / ID: 1ed3 | ||||||
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Title | CRYSTAL STRUCTURE OF RAT MINOR HISTOCOMPATIBILITY ANTIGEN COMPLEX RT1-AA/MTF-E. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / major histocompatibility complex / rat minor histocompatibility complex / MHC / immunology / peptide antigen presentation / cellular immunity / cell surface receptor / T cell receptor ligand | ||||||
Function / homology | Function and homology information Formation of ATP by chemiosmotic coupling / Cristae formation / Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / : / Neutrophil degranulation ...Formation of ATP by chemiosmotic coupling / Cristae formation / Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / : / Neutrophil degranulation / mitochondrial proton-transporting ATP synthase complex / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / response to hyperoxia / response to cadmium ion / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / proton-transporting ATP synthase activity, rotational mechanism / lumenal side of endoplasmic reticulum membrane / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / iron ion transport / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / immune response / response to xenobiotic stimulus / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Speir, J.A. / Stevens, J. / Joly, E. / Butcher, G.W. / Wilson, I.A. | ||||||
Citation | Journal: Immunity / Year: 2001 Title: Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa. Authors: Speir, J.A. / Stevens, J. / Joly, E. / Butcher, G.W. / Wilson, I.A. #1: Journal: J.Immunol. / Year: 1997 Title: Identification of the rat maternally transmitted minor histocompatibility antigen Authors: Bhuyan, P.K. / Young, L.L. / Lindahl, K.F. / Butcher, G.W. #2: Journal: J.Biol.Chem. / Year: 1998 Title: Efficient generation of major histocompatibility complex class I-peptide complexes using synthetic peptide libraries Authors: Stevens, J. / Wiesmuller, K.-H. / Barker, P.J. / Walden, P. / Bucher, G.W. / Joly, E. #3: Journal: Eur.J.Biochem. / Year: 1998 Title: Peptide length preferences for rat and mouse MHC class I molecules using random peptide libraries Authors: Stevens, J. / Wiesmuller, K.-H. / Walden, P. / Joly, E. #4: Journal: Immunity / Year: 1996 Title: The rat cim effect: TAP allele-dependent changes in a class I MHC anchor motif and evidence against C-terminal trimming of peptides in the ER Authors: Powis, S.J. / Young, L.L. / Joly, E. / Barker, P.J. / Richardson, L. / Brandt, R.P. / Melief, C.J. / Howard, J.C. / Butcher, G.W. #5: Journal: Immunogenetics / Year: 1995 Title: An analysis of the antigen binding site of RT1-Aa suggests an allele-specific motif Authors: Thorpe, C.J. / Moss, D.S. / Powis, S.J. / Howard, J.C. / Butcher, G.W. / Travers, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ed3.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ed3.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ed3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1ed3 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1ed3 | HTTPS FTP |
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-Related structure data
Related structure data | 2clrS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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Details | There are two heterotrimeric biological assemblies in the asymmetric unit constructed from chains A, B, and C, or chains D, E, and F. |
-Components
#1: Protein | Mass: 32045.551 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / References: UniProt: P16391 #2: Protein | Mass: 11652.282 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET-22B / Production host: Escherichia coli (E. coli) / References: UniProt: P07151 #3: Protein/peptide | Mass: 1533.773 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-41 OF RAT ATPASE 6 / Source method: obtained synthetically / Details: This sequence occurs naturally in rats / References: UniProt: P05504 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 48.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M morpholine ethansulfonic acid (MES), 0.2M ammonium sulfate, 15-20% MPEG 5000, 0.025M beta-octyl-glucoside, 0.5% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 9, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. all: 28978 / Num. obs: 28978 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2757 / % possible all: 91.2 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 91.2 % / Num. unique obs: 2757 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CLR Resolution: 2.55→19.89 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: Engh & Huber as implemented in X-PLOR and CNS
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Solvent computation | Bsol: 33.8132 Å2 / ksol: 0.368077 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.89 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.55→2.64 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 7.5 % / Rfactor obs: 0.224 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.37 / % reflection Rfree: 7.5 % / Rfactor Rwork: 0.319 / Rfactor obs: 0.319 |