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- PDB-3bp4: The high resolution crystal structure of HLA-B*2705 in complex wi... -
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Basic information
Entry | Database: PDB / ID: 3bp4 | ||||||
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Title | The high resolution crystal structure of HLA-B*2705 in complex with a Cathepsin A signal sequence peptide pCatA | ||||||
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![]() | IMMUNE SYSTEM / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / Beta-2-microglobulin / b2m / Cathepsin A / pCatA / Ankylosing Spondylitis / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Carboxypeptidase / Hydrolase / Lysosome / Protease / Zymogen | ||||||
Function / homology | ![]() carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / negative regulation of chaperone-mediated autophagy / regulation of T cell anergy ...carboxypeptidase C / Defective NEU1 causes sialidosis / serine-type carboxypeptidase activity / Sialic acid metabolism / regulation of chaperone-mediated autophagy / Glycosphingolipid catabolism / regulation of interleukin-12 production / regulation of dendritic cell differentiation / negative regulation of chaperone-mediated autophagy / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / carboxypeptidase activity / enzyme activator activity / MHC class II antigen presentation / lysosomal lumen / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / 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 / regulation of protein stability / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / defense response / 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 / specific granule lumen / recycling endosome membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / azurophil granule lumen / 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 / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / lysosome / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
![]() | ![]() Title: Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens Authors: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Merino, E. / Lopez de Castro, J.A. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.7 KB | Display | ![]() |
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PDB format | ![]() | 79.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bp7SC ![]() 3bvnC ![]() 3bxnC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31928.160 Da / Num. of mol.: 1 Fragment: HLA-B*2705 extracellular domain, UNP residues 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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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.) ![]() ![]() ![]() | ||
#3: Protein/peptide | Mass: 982.198 Da / Num. of mol.: 1 / Fragment: Cathepsin A signal sequence, UNP residues 2-10 / Source method: obtained synthetically Details: Cathepsin A signal sequence peptide chemically synthesized; This sequence occurs naturally in humans. Source: (synth.) ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 23% PEG 8000, 0.1M Tris buffer pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 19, 2006 / Details: Mirrors |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 38830 / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Χ2: 1.12 / Net I/σ(I): 12.41 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.08 / Num. unique all: 3323 / Rsym value: 0.311 / Χ2: 0.999 / % possible all: 83.7 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3BP7 Resolution: 1.85→46.63 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.899 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.192 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→46.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.849→1.897 Å / Total num. of bins used: 20
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