+Open data
-Basic information
Entry | Database: PDB / ID: 4x5x | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | HLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W) | |||||||||||||||
Components |
| |||||||||||||||
Keywords | IMMUNE SYSTEM / MHC II / SELF ANTIGEN / INVARIANT CHAIN / CLIP | |||||||||||||||
Function / homology | Function and homology information regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / 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 / positive regulation of kinase activity / inflammatory response to antigenic stimulus / transport vesicle membrane / intermediate filament / 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 / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / 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 / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.199 Å | |||||||||||||||
Authors | Guenther, S. / Freund, C. | |||||||||||||||
Funding support | Germany, 4items
| |||||||||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: MHC class II complexes sample intermediate states along the peptide exchange pathway. Authors: Wieczorek, M. / Sticht, J. / Stolzenberg, S. / Gunther, S. / Wehmeyer, C. / El Habre, Z. / Alvaro-Benito, M. / Noe, F. / Freund, C. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4x5x.cif.gz | 163.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4x5x.ent.gz | 127.9 KB | Display | PDB format |
PDBx/mmJSON format | 4x5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x5x ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x5x | HTTPS FTP |
---|
-Related structure data
Related structure data | 4x5wC 1dlhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | The biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D) |
-Components
#1: Protein | Mass: 22353.223 Da / Num. of mol.: 2 / Fragment: extracellular, UNP residues 26-217 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903 #2: Protein | Mass: 25761.893 Da / Num. of mol.: 2 / Fragment: extracellular, UNP residues 30-227 / Mutation: N82A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET24D / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04229, UniProt: P01911*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.16 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å | ||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2012 / 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: 3.199→34.25 Å / Num. obs: 14844 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 39.17 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.192 / Net I/σ(I): 5.5 / Num. measured all: 45860 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1dlh Resolution: 3.199→34.247 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.96 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.16 Å2 / Biso mean: 44.0737 Å2 / Biso min: 10.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.199→34.247 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
|