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- PDB-4pgd: MHC Class I in complex with modified Sendai virus nucleoprotein p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pgd | ||||||
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Title | MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGNYPAF | ||||||
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![]() | IMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / IMMUNE RESPONSE / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | ![]() 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 / 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 ...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 / 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 / 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 / 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 / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / 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 / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to bacterium / ribonucleoprotein complex / immune response / lysosomal membrane / external side of plasma 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 | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Celie, P. / Joosten, R.P. / Perrakis, A. / Neefjes, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The first step of peptide selection in antigen presentation by MHC class I molecules. Authors: Garstka, M.A. / Fish, A. / Celie, P.H. / Joosten, R.P. / Janssen, G.M. / Berlin, I. / Hoppes, R. / Stadnik, M. / Janssen, L. / Ovaa, H. / van Veelen, P.A. / Perrakis, A. / Neefjes, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.7 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pg9C ![]() 4pgbC ![]() 4pgcC ![]() 4pgeC ![]() 2vabS C: citing same article ( 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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Details | The biological unit is the same as asymmetric unit |
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Components
#1: Protein | Mass: 34956.996 Da / Num. of mol.: 1 / Fragment: heavy chain, UNP residues 22-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 11835.555 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 983.076 Da / Num. of mol.: 1 / Fragment: peptide 324-332 / Mutation: L332F / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis / Source: (synth.) ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→74.074 Å / Num. all: 15630 / Num. obs: 15630 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.42 Å2 / Rpim(I) all: 0.082 / Rrim(I) all: 0.162 / Rsym value: 0.139 / Net I/av σ(I): 4.688 / Net I/σ(I): 10.6 / Num. measured all: 58928 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VAB Resolution: 2.7→45.22 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.246 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.683 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.5 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.81 Å2
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Refinement step | Cycle: final / Resolution: 2.7→45.22 Å
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Refine LS restraints |
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