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Yorodumi- PDB-1k2d: Crystal structure of the autoimmune MHC class II I-Au complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k2d | |||||||||
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Title | Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class II / I-Au / H-2u / autoimmune disease / unique register / experimental autoimmune encephalomyelitis / myelin basic protein | |||||||||
Function / homology | Function and homology information structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / compact myelin / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / EGR2 and SOX10-mediated initiation of Schwann cell myelination / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production ...structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / compact myelin / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / antigen processing and presentation of peptide antigen / EGR2 and SOX10-mediated initiation of Schwann cell myelination / membrane organization / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of T cell differentiation / maintenance of blood-brain barrier / antigen processing and presentation / negative regulation of T cell proliferation / substantia nigra development / myelination / multivesicular body / central nervous system development / cell periphery / sensory perception of sound / response to toxic substance / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of interleukin-6 production / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MAPK cascade / positive regulation of T cell activation / myelin sheath / MHC class II protein complex binding / late endosome membrane / chemical synaptic transmission / protease binding / adaptive immune response / lysosome / calmodulin binding / early endosome / immune response / lysosomal membrane / external side of plasma membrane / neuronal cell body / synapse / lipid binding / protein-containing complex binding / Golgi apparatus / cell surface / protein-containing complex / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | He, X.L. / Radu, C. / Ward, E.S. / Garcia, K.C. | |||||||||
Citation | Journal: IMMUNITY / Year: 2002 Title: Structural snapshot of aberrant antigen presentation linked to autoimmunity: the immunodominant epitope of MBP complexed with I-Au Authors: He, X.L. / Radu, C. / Sidney, J. / Sette, A. / Ward, E.S. / Garcia, K.C. | |||||||||
History |
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Remark 999 | SEQUENCE THE C-terminus of the MBP PEPTIDE IS LINKED TO A SYNTHETIC LINKER PEPTIDE, AND ARE Listed ...SEQUENCE THE C-terminus of the MBP PEPTIDE IS LINKED TO A SYNTHETIC LINKER PEPTIDE, AND ARE Listed in the seqres as CHAIN ID P. THE C-terminus of the LINKER PEPTIDE IS LINKED TO THE N-terminus of the BETA CHAIN. THE LINKER PEPTIDE WAS NOT SEEN IN THE ELECTRON DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k2d.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k2d.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/1k2d ftp://data.pdbj.org/pub/pdb/validation_reports/k2/1k2d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21468.809 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR ALPHA-1 AND ALPHA-2 DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14438 | ||
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#2: Protein | Mass: 22495.164 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR BETA-1 AND BETA-2 DOMAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P06344 | ||
#3: Protein/peptide | Mass: 2319.395 Da / Num. of mol.: 1 / Fragment: 11 residue peptide with 8 residue linker peptide / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the MBP portion of the peptide is naturally found in Homo sapiens (human). References: GenBank: 14763906, UniProt: P02686*PLUS | ||
#4: Sugar | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.18 % | ||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: MPEG 5000, sodium chloride, citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K | ||||||||||||||||||
Crystal grow | *PLUS pH: 4.5 | ||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 21, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 26280 / Num. obs: 26280 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3825 / % possible all: 98.7 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 144694 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / % possible obs: 98.5 % / Rmerge(I) obs: 0.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IAKJ Resolution: 2.2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 50.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.029
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Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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