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Yorodumi- PDB-1es0: CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1es0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) PEPTIDE 207-220 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN / CLASS II MHC I-A(G7) | ||||||
Function / homology | Function and homology information GABA synthesis / gamma-aminobutyrate shunt / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / response to caloric restriction ...GABA synthesis / gamma-aminobutyrate shunt / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / inhibitory synapse / response to caloric restriction / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / glutamate binding / antigen processing and presentation / GABA-ergic synapse / negative regulation of T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / response to cocaine / response to progesterone / synaptic vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / pyridoxal phosphate binding / MHC class II protein complex binding / late endosome membrane / presynaptic membrane / cellular response to hypoxia / chemical synaptic transmission / adaptive immune response / lysosome / response to xenobiotic stimulus / external side of plasma membrane / Golgi membrane / axon / lysosomal membrane / neuronal cell body / protein-containing complex binding / perinuclear region of cytoplasm / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Corper, A.L. / Teyton, L. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 2000 Title: A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes. Authors: Corper, A.L. / Stratmann, T. / Apostolopoulos, V. / Scott, C.A. / Garcia, K.C. / Kang, A.S. / Wilson, I.A. / Teyton, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1es0.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1es0.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 1es0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/1es0 ftp://data.pdbj.org/pub/pdb/validation_reports/es/1es0 | HTTPS FTP |
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-Related structure data
Related structure data | 1iakS 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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Unit cell |
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-Components
#1: Protein | Mass: 21623.129 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P04228 |
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#2: Protein | Mass: 25563.430 Da / Num. of mol.: 1 / Fragment: PEPTIDE (RESIDUES 222-235) + BETA CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q05329, GenBank: 387435 |
#3: Water | ChemComp-HOH / |
Sequence details | THIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II ALLELE I- ...THIS ENTRY CONTAINS COORDINATE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-18% PEG 4000, 0.2 M LICL (PH 6.6), 1% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: unknown / Details: seeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.96 Å / Num. obs: 15754 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 51.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.353 / % possible all: 99.6 |
Reflection | *PLUS Num. measured all: 66107 / Rmerge(I) obs: 0.068 |
Reflection shell | *PLUS % possible obs: 99.6 % / Rmerge(I) obs: 0.353 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: I-A(K) - PDB CODE 1IAK Resolution: 2.6→39.96 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.63 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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