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Yorodumi- PDB-1a6a: THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a6a | ||||||
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Title | THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3 | ||||||
Components |
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Keywords | COMPLEX (TRANSMEMBRANE/GLYCOPROTEIN) / MHC GLYCOPROTEIN / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex | ||||||
Function / homology | Function and homology information immunoglobulin production involved in immunoglobulin-mediated immune response / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / : / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding ...immunoglobulin production involved in immunoglobulin-mediated immune response / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / : / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / regulation of interleukin-4 production / regulation of interleukin-10 production / T cell activation involved in immune response / 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 / positive regulation of type 2 immune response / autolysosome membrane / T cell selection / positive regulation of prostaglandin biosynthetic process / regulation of T-helper cell differentiation / negative thymic T cell selection / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / humoral immune response mediated by circulating immunoglobulin / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive regulation of memory T cell differentiation / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / cytokine receptor activity / vacuole / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / intermediate filament / regulation of macrophage activation / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nitric-oxide synthase binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / plasma membrane => GO:0005886 / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / antigen processing and presentation / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / chaperone cofactor-dependent protein refolding / Generation of second messenger molecules / immunological synapse / PD-1 signaling / immunoglobulin mediated immune response / epidermis development / T cell receptor binding / type II interferon-mediated signaling pathway / negative regulation of T cell proliferation / detection of bacterium / positive regulation of chemokine production / positive regulation of B cell proliferation / negative regulation of inflammatory response to antigenic stimulus / protein folding chaperone / MHC class II antigen presentation / multivesicular body / lysosomal lumen / trans-Golgi network membrane / negative regulation of cell migration / clathrin-coated endocytic vesicle membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / protein tetramerization / intracellular protein transport / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / positive regulation of fibroblast proliferation / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Ghosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C. | ||||||
Citation | Journal: Nature / Year: 1995 Title: The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Authors: Ghosh, P. / Amaya, M. / Mellins, E. / 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 | 1a6a.cif.gz | 88.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6a.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 1a6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a6a_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 1a6a_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 1a6a_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1a6a_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6a ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6a | HTTPS FTP |
-Related structure data
Related structure data | 1dlhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20469.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P01903 | ||
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#2: Protein | Mass: 21935.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P01912, UniProt: P01911*PLUS | ||
#3: Protein/peptide | Mass: 1676.118 Da / Num. of mol.: 1 / Fragment: CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANE / References: UniProt: P04233 | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknownDetails: conditions similar to: Gorga, J.C., (1991) Res. Immun., 142, 401. | ||||||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.918 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→15 Å / Num. obs: 14428 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.75→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.3 / % possible all: 97.2 |
Reflection | *PLUS Num. obs: 13021 |
Reflection shell | *PLUS % possible obs: 97.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DLH Resolution: 2.75→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP ...Details: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109, 172, AND 189).
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Displacement parameters | Biso mean: 47.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.86 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.373 |