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- PDB-1jwu: Crystal Structure of the Complex of the MHC Class II Molecule HLA... -
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Basic information
Entry | Database: PDB / ID: 1jwu | ||||||
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Title | Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1 (HA peptide 306-318) with the superantigen SEC3 Variant 3B2 | ||||||
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![]() | IMMUNE SYSTEM / HLA-DR1 alpha subunit / HLA-DR1 beta subunit / Mutation | ||||||
Function / homology | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane / lysosomal membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sundberg, E.J. / Andersen, P.S. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. | ||||||
![]() | ![]() Title: Structural, energetic, and functional analysis of a protein-protein interface at distinct stages of affinity maturation Authors: Sundberg, E.J. / Andersen, P.S. / Schlievert, P.M. / Karjalainen, K. / Mariuzza, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 135.7 KB | Display | ![]() |
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PDB format | ![]() | 111 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 21155.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 22080.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1506.807 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The Peptide was Chemically Synthesized |
#4: Protein | Mass: 27721.068 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.72 Å3/Da / Density % sol: 73.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Sodium Acetate, Ethylene Glycol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97813 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 58678 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2 / Rsym value: 0.067 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.421 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 172353 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.421 |
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Processing
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Refinement | Resolution: 2.3→14.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 160762.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.8198 Å2 / ksol: 0.342412 e/Å3 | |||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 4.3 % / Rfactor Rwork: 0.2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.38 Å |