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Yorodumi- PDB-3ln5: Crystal structure of HLA-B*4104 in complex with a 11mer self-pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ln5 | ||||||
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Title | Crystal structure of HLA-B*4104 in complex with a 11mer self-peptide derived from S-methyl-5-thioadenosine phosphorylase | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin domain / Immune response / Major Histocompatibility Complex Class I / MHC-I peptide complex / peptide-binding motifs / Disulfide bond | ||||||
Function / homology | Function and homology information Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / nucleobase-containing compound metabolic process / purine ribonucleoside salvage ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / regulation of interleukin-6 production / response to testosterone / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / methylation / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Theodossis, A. / Gras, S. / Rossjohn, J. | ||||||
Citation | Journal: Haematologica / Year: 2011 Title: The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family Authors: Bade-Doding, C. / Theodossis, A. / Gras, S. / Kjer-Nielsen, L. / Eiz-Vesper, B. / Seltsam, A. / Huyton, T. / Rossjohn, J. / McCluskey, J. / Blasczyk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ln5.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ln5.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ln5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/3ln5 ftp://data.pdbj.org/pub/pdb/validation_reports/ln/3ln5 | HTTPS FTP |
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-Related structure data
Related structure data | 3ln4C 1syvS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31771.967 Da / Num. of mol.: 1 / Fragment: extracellular domains, UNP residues 25-298' Source method: isolated from a genetically manipulated source Details: B*4104 allele (W95L/R97S/V103L/N114D polymorphic variant) Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P30479, UniProt: P01889*PLUS |
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcRT7 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1255.377 Da / Num. of mol.: 1 / Fragment: UNP residues 227-237 / Source method: obtained synthetically / Details: Fmoc peptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13126 |
#4: 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: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M citrate pH 5.6, 14-20% PEG 4000, 0.2M NH4OAc, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98133 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 22, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98133 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→55.1 Å / Num. all: 35909 / Num. obs: 35909 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.48 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.79 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 4.26 / Num. unique all: 4620 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SYV Resolution: 1.9→34.044 Å / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.853 / SU ML: 0.25 / σ(F): 0.02 / Phase error: 21.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.162 Å2 / ksol: 0.325 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.45 Å2 / Biso mean: 21.237 Å2 / Biso min: 5.35 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→34.044 Å
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Refine LS restraints |
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LS refinement shell |
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