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- PDB-4ah2: HLA-DR1 with covalently linked CLIP106-120 in canonical orientation -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ah2 | ||||||
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Title | HLA-DR1 with covalently linked CLIP106-120 in canonical orientation | ||||||
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![]() | IMMUNE SYSTEM / MHC II / SELF ANTIGEN / INVARIANT CHAIN / CLIP | ||||||
Function / homology | ![]() 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 ...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 / autolysosome membrane / positive regulation of type 2 immune response / T cell selection / regulation of T-helper cell differentiation / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / 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 / 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 / vacuole / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / cytokine receptor activity / regulation of macrophage activation / transport vesicle membrane / intermediate filament / 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 / cytokine binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / antigen processing and presentation / negative regulation of DNA damage response, signal transduction by p53 class mediator / 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 / detection of bacterium / negative regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / multivesicular body / negative regulation of cell migration / lysosomal lumen / trans-Golgi network 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 / 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 / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / positive regulation of immune response / positive regulation of fibroblast proliferation / late endosome Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schlundt, A. / Guenther, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Heinemann, U. / Freund, C. | ||||||
![]() | ![]() Title: Peptide Linkage to the Alpha-Subunit of Mhcii Creates a Stably Inverted Antigen Presentation Complex. Authors: Schlundt, A. / Gunther, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Heinemann, U. / Freund, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.5 KB | Display | ![]() |
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PDB format | ![]() | 72.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451 KB | Display | ![]() |
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Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4aenC ![]() 3pdoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22353.223 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 26-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 25749.902 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 106-120,30-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | CLIP WAS ATTACHED TO THE N-TERMINUS OF MHC BETA-CHAIN DURING EXPRESSION | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.44 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.2 M LICL, 20% (W/V) PEG6000, 0.1 M HEPES, PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH MX-225 / Detector: CCD / Date: Jan 13, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→32.84 Å / Num. obs: 21133 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.36→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3PDO Resolution: 2.36→32.833 Å / SU ML: 0.76 / σ(F): 1.99 / Phase error: 22.41 / Stereochemistry target values: ML Details: RESIDUES A0 TO A3, A181 TO A192, B-16 TO B-1, B105 TO B110, B190 TO B198 ARE MISSING COMPLETELY DUE TO DISORDER, RESIDUES B111, B112, B166 COULD ONLY BE MODELED TO THE CBETA-ATOM DUE TO DISORDER
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.165 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→32.833 Å
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Refine LS restraints |
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LS refinement shell |
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