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Yorodumi- PDB-1nam: MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nam | |||||||||
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Title | MURINE ALLOREACTIVE SCFV TCR-PEPTIDE-MHC CLASS I MOLECULE COMPLEX | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / T cell receptor / class I MHC / H-2Kb / TCR-pMHC complex / alloreactivity / crossreactivity | |||||||||
Function / homology | Function and homology information 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 / T cell receptor complex / helical viral capsid / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development ...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 / T cell receptor complex / helical viral capsid / 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 / peptide binding / 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 / lumenal side of endoplasmic reticulum membrane / 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 / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / 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 / iron ion transport / T cell differentiation in thymus / protein refolding / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to bacterium / ribonucleoprotein complex / immune response / external side of plasma membrane / lysosomal membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B. | |||||||||
Citation | Journal: Nat.Immunol. / Year: 2003 Title: CDR3 loop flexibility contributes to the degeneracy of TCR recognition Authors: Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B. #1: Journal: Nat.Immunol. / Year: 2000 Title: Crystal structure of a T cell receptor bound to an allogeneic MHC molecule Authors: Reiser, J.-B. / Darnault, C. / Guimezanes, A. / Gregoire, C. / Mosser, T. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Malissen, B. / Housset, D. / Mazza, G. #2: Journal: Immunity / Year: 2002 Title: A T-Cell Receptor CDR3Beta Loop Undergoes Conformational Changes of Unprecedented Magnitude Upon Binding to a Peptide/MHC Class I Complex Authors: Reiser, J.-B. / Gregoire, C. / Darnault, C. / Mosser, T. / Guimezanes, A. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Mazza, G. / Malissen, B. / Housset, D. #3: Journal: Science / Year: 1992 Title: Crystal Structures of Two Viral Peptides in Complex with Murine MHC Class I H-2Kb Authors: Fremont, D.H. / Matsumura, M. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. | |||||||||
History |
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Remark 999 | SEQUENCE Author states the sequence of the BM3.3 TCR has never been deposited in any database, ...SEQUENCE Author states the sequence of the BM3.3 TCR has never been deposited in any database, however it has been published in the following paper: Couez D, Malissen M, Buferne M, Schmitt-Verhulst AM, Malissen B. (1991) Each of the two productive T cell receptor alpha-gene rearrangements found in both the A10 and BM 3.3 T cell clones give rise to an alpha chain which can contribute to the constitution of a surface-expressed alpha beta dimer. Int Immunol. 3(7):719-29. Moreover, TCR sequences are the result of V,J and C genes recombination for the alpha chain, V, D, J, C genes recombination for the beta chain. The BM3.3 TCR variable domain is made of the following segments: TRAV16*01, TRAJ32 for the Valpha and Jalpha segments (chain A) TRBV1*01, TRBJ1-3*01 for the Vbeta, Jbeta segments (chain B). Author states the TCR variable domain is produced as a single chain Fv fragment. The Valpha domain (chain A) C-terminus is artificially connected to the Vbeta domain (chain B) N-terminus by the mean of a flexible hydrophilic linker (sequence GSADDASADDAKKDAAKKDDAKKDDAKKDGS) for wich no electron density is observed. Since this linker has no biological role and does not interfere with TCR recognition, it has not been incorporated in the model and the sequence record. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nam.cif.gz | 142.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nam.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nam_validation.pdf.gz | 823.3 KB | Display | wwPDB validaton report |
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Full document | 1nam_full_validation.pdf.gz | 860 KB | Display | |
Data in XML | 1nam_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 1nam_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/na/1nam ftp://data.pdbj.org/pub/pdb/validation_reports/na/1nam | HTTPS FTP |
-Related structure data
Related structure data | 1nanC 1fo0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-BM3.3 T Cell Receptor ... , 2 types, 2 molecules AB
#1: Protein | Mass: 12945.639 Da / Num. of mol.: 1 / Fragment: Fv Fragment, Variable Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): myeloma cells / Production host: Mus musculus (house mouse) / References: UniProt: Q5R1F1*PLUS |
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#2: Protein | Mass: 13064.964 Da / Num. of mol.: 1 / Fragment: Fv Fragment, Variable Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): myeloma cells / Production host: Mus musculus (house mouse) / References: UniProt: P04214*PLUS |
-Protein , 2 types, 2 molecules HL
#3: Protein | Mass: 31777.438 Da / Num. of mol.: 1 / Fragment: Extracellular Domains (alpha1, alpha2, alpha3) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901 |
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#5: Protein | Mass: 11835.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887 |
-Protein/peptide / Sugars / Non-polymers , 3 types, 103 molecules P
#4: Protein/peptide | Mass: 956.078 Da / Num. of mol.: 1 Fragment: Vesicular Stomatitis Virus Nucleoprotein fragment, residues (52-59) Source method: obtained synthetically Details: The 8-residue peptide of vesicular stomatitis virus was chemically synthesized. References: UniProt: P11212 |
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#6: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#7: 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: 3.66 Å3/Da / Density % sol: 66.17 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: PEG6000 13-17%, MgAc 0.1M, NaCl 0-0.1M, Hepes 0.1M, pH 7.0 to 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→35.1 Å / Num. all: 29887 / Num. obs: 29887 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 60.2 Å2 / Rsym value: 0.083 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2033 / Rsym value: 0.437 / % possible all: 99.2 |
Reflection | *PLUS Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 99.2 % / Rmerge(I) obs: 0.437 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FO0 Resolution: 2.7→12 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 56.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.79 Å
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Refinement | *PLUS Rfactor obs: 0.237 / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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