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Yorodumi- PDB-4pgc: MHC Class I in complex with modified Sendai virus nucleoprotein p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pgc | ||||||
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Title | MHC Class I in complex with modified Sendai virus nucleoprotein peptide FAPGN(3,5-diiodotyrosine)PAL | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE / IMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / IMMUNE RESPONSE / IMMUNE SYSTEM-PEPTIDE complex | ||||||
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 / 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 / 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 / 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) Escherichia coli (E. coli) Sendai virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Celie, P. / Joosten, R.P. / Perrakis, A. / Neefjes, J. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pgc.cif.gz | 329.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pgc.ent.gz | 266.4 KB | Display | PDB format |
PDBx/mmJSON format | 4pgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pgc_validation.pdf.gz | 489.2 KB | Display | wwPDB validaton report |
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Full document | 4pgc_full_validation.pdf.gz | 492.3 KB | Display | |
Data in XML | 4pgc_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 4pgc_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/4pgc ftp://data.pdbj.org/pub/pdb/validation_reports/pg/4pgc | HTTPS FTP |
-Related structure data
Related structure data | 4pg9C 4pgbC 4pgdC 4pgeC 1rjzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | There are 2 biological units in the asymmetric unit (chains A, B, and C and chains D, E, and F). Chain H is an unknown helical fragment that is not part of the biological unit. |
-Components
-Protein , 2 types, 4 molecules ADBE
#1: Protein | Mass: 34956.996 Da / Num. of mol.: 2 / Fragment: heavy chain, UNP residues 22-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01901 #2: Protein | Mass: 11835.555 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01887 |
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-Protein/peptide , 2 types, 3 molecules CFH
#3: Protein/peptide | Mass: 1200.853 Da / Num. of mol.: 2 / Fragment: peptide 324-332 / Mutation: Y329(TYI) / Source method: obtained synthetically / Details: Solid Phase Peptide Synthesis / Source: (synth.) Sendai virus / References: UniProt: O57286*PLUS #4: Protein/peptide | | Mass: 1214.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Author are quite sure that the fragment is not from H-2Kb or beta2 macroglobulin. Because E-coli was the expression system, this was the most likely source. Source: (natural) Escherichia coli (E. coli) / Strain: BL21(DE3)pLysS |
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-Non-polymers , 2 types, 63 molecules
#5: Chemical | ChemComp-GOL / #6: 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: 2.55 Å3/Da / Density % sol: 51.85 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→83.108 Å / Num. all: 43356 / Num. obs: 43356 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.091 / Rsym value: 0.077 / Net I/av σ(I): 8.909 / Net I/σ(I): 12 / Num. measured all: 152881 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rjz Resolution: 2.3→83.108 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / Matrix type: sparse / WRfactor Rfree: 0.227 / WRfactor Rwork: 0.195 / SU B: 17.453 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.17 Å2 / Biso mean: 39.719 Å2 / Biso min: 18.45 Å2
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Refinement step | Cycle: final / Resolution: 2.3→83.108 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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