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Yorodumi- PDB-1fv1: STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fv1 | ||||||
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Title | STRUCTURAL BASIS FOR THE BINDING OF AN IMMUNODOMINANT PEPTIDE FROM MYELIN BASIC PROTEIN IN DIFFERENT REGISTERS BY TWO HLA-DR2 ALLELES | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC class II DR2a | ||||||
Function / homology | Function and homology information compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 ...compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 / EGR2 and SOX10-mediated initiation of Schwann cell myelination / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / membrane organization / positive regulation of memory T cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / transport vesicle membrane / polysaccharide binding / maintenance of blood-brain barrier / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / substantia nigra development / MHC class II antigen presentation / myelination / trans-Golgi network membrane / clathrin-coated endocytic vesicle membrane / central nervous system development / cell periphery / lumenal side of endoplasmic reticulum membrane / sensory perception of sound / ER to Golgi transport vesicle membrane / response to toxic substance / cognition / peptide antigen assembly with MHC class II protein complex / 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 / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / MAPK cascade / positive regulation of T cell activation / Downstream TCR signaling / myelin sheath / MHC class II protein complex binding / early endosome membrane / late endosome membrane / protease binding / chemical synaptic transmission / adaptive immune response / calmodulin binding / lysosome / immune response / Golgi membrane / lysosomal membrane / neuronal cell body / lipid binding / synapse / cell surface / protein-containing complex / extracellular exosome / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Li, H. / Mariuzza, A.R. / Li, Y. / Martin, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structural basis for the binding of an immunodominant peptide from myelin basic protein in different registers by two HLA-DR2 proteins. Authors: Li, Y. / Li, H. / Martin, R. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fv1.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fv1.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fv1_validation.pdf.gz | 482.6 KB | Display | wwPDB validaton report |
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Full document | 1fv1_full_validation.pdf.gz | 502.5 KB | Display | |
Data in XML | 1fv1_validation.xml.gz | 37 KB | Display | |
Data in CIF | 1fv1_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/1fv1 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/1fv1 | HTTPS FTP |
-Related structure data
Similar structure data |
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-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
-MAJOR HISTOCOMPATIBILITY COMPLEX ... , 2 types, 4 molecules ADBE
#1: Protein | Mass: 21084.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: P01903 #2: Protein | Mass: 22231.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: Q30154 |
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-Protein/peptide , 1 types, 2 molecules CF
#3: Protein/peptide | Mass: 2278.627 Da / Num. of mol.: 2 / Fragment: RESIDUES 86-105 / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: P02686 |
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-Non-polymers , 3 types, 499 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.05 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6.5 Details: 2/3 dilution of 30% PEG 8000, 0.1M sodium cacodylate, pH6.5, 0.2M ammonium sulfate, EVAPORATION, temperature 298.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 63997 / Num. obs: 49803 / % possible obs: 0.78 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 0.081 |
Reflection shell | Resolution: 1.9→1.99 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.349 / % possible all: 0.76 |
Reflection | *PLUS Num. obs: 63997 / % possible obs: 90.8 % / Num. measured all: 181399 |
Reflection shell | *PLUS % possible obs: 75.6 % / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Resolution: 1.9→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→100 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.5 |