+Open data
-Basic information
Entry | Database: PDB / ID: 1k5n | ||||||
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Title | HLA-B*2709 BOUND TO NONA-PEPTIDE M9 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC(MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA(HUMAN LEUKOCYTE ANTIGEN) | ||||||
Function / homology | Function and homology information regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / 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 / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / defense response / 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 / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / 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 / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å | ||||||
Authors | Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: HLA-B27 Subtypes Differentially Associated with Disease Exhibit Subtle Structural Alterations Authors: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: Journal: J.IMMUNOL. / Year: 1994 Title: Identification of a Novel Hla-B27 Subtype by Restriction Analysis of a Cytotoxic Gamma Delta T Cell Clone Authors: Del Porto, P. / D'Amato, M. / Fiorillo, M.T. / Tuosto, L. / Piccolella, E. / Sorrention, R. #2: Journal: Nature / Year: 1991 Title: The Structure of Hla-B27 Reveals Nonamer Self-Peptides Bound in an Extended Conformation Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #3: Journal: CELL(CAMBRIDGE,MASS.) / Year: 1992 Title: The Three-Dimensional Structure of Hla-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc Authors: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k5n.cif.gz | 221 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k5n.ent.gz | 175.2 KB | Display | PDB format |
PDBx/mmJSON format | 1k5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/1k5n ftp://data.pdbj.org/pub/pdb/validation_reports/k5/1k5n | HTTPS FTP |
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-Related structure data
Related structure data | 1jgeSC 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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Details | The biologically assembly is a heterotrimeric complex consisting of one HLA-B*2709(heavy) chain, one beta-2-microglobulin(light) chain and one nonameric model peptide m9. |
-Components
#1: Protein | Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: HLA-B*2709 heavy chain, extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B or HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P03989, UniProt: P01889*PLUS | ||
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 | ||
#3: Protein/peptide | Mass: 906.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This peptide was chemically synthesised. | ||
#4: Chemical | #5: 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: 2.6 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PEG 8000, Bicine, NaCl, glycerol as cryo protectant, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Details: used cross-seeding | |||||||||||||||||||||||||||||||||||
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: 0.9393 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2001 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.09→19.1 Å / Num. all: 187545 / Num. obs: 187545 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.09→1.12 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12377 / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 1.09 Å / Lowest resolution: 19.1 Å / Redundancy: 4.7 % |
Reflection shell | *PLUS % possible obs: 96.8 % / Redundancy: 2.9 % / Num. unique obs: 12377 / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JGE (HLA-B*2705:m9), with Asp-A116 truncated to Ala Resolution: 1.09→19.1 Å / SU B: 0.79443 / SU ML: 0.02034 / Isotropic thermal model: anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03234 / ESU R Free: 0.03298 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 11.517 Å2
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Refinement step | Cycle: LAST / Resolution: 1.09→19.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.09→1.13 Å
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Refinement | *PLUS Lowest resolution: 19.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.148 / Rfactor Rwork: 0.123 | ||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_deg / Dev ideal: 2.26 | ||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.12 Å / Rfactor Rfree: 0.18 |