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Yorodumi- PDB-1q69: Solution structure of T-cell surface glycoprotein CD8 alpha chain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q69 | ||||||
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Title | Solution structure of T-cell surface glycoprotein CD8 alpha chain and Proto-oncogene tyrosine-protein kinase LCK fragments | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/TRANSFERASE / Peptide-peptide complex / helix-helix interaction / zinc coordination / beta hairpin / MEMBRANE PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information cytotoxic T cell differentiation / MHC class I protein complex binding / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / T cell mediated immunity / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding ...cytotoxic T cell differentiation / MHC class I protein complex binding / regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / Fc-gamma receptor signaling pathway / T cell mediated immunity / CD28 co-stimulation / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / T cell receptor complex / Regulation of KIT signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / leukocyte migration / phospholipase activator activity / CD8 receptor binding / pericentriolar material / positive regulation of T cell receptor signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / MHC class I protein binding / plasma membrane raft / antigen processing and presentation / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / phospholipase binding / RHOH GTPase cycle / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / coreceptor activity / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of intrinsic apoptotic signaling pathway / peptidyl-tyrosine autophosphorylation / release of sequestered calcium ion into cytosol / extrinsic component of cytoplasmic side of plasma membrane / GPVI-mediated activation cascade / cell surface receptor protein tyrosine kinase signaling pathway / T cell costimulation / T cell activation / phosphotyrosine residue binding / SH2 domain binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / platelet activation / peptidyl-tyrosine phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / activation of cysteine-type endopeptidase activity involved in apoptotic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / positive regulation of T cell activation / PIP3 activates AKT signaling / DAP12 signaling / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / adaptive immune response / cell surface receptor signaling pathway / receptor complex / intracellular signal transduction / response to xenobiotic stimulus / immune response / membrane raft / external side of plasma membrane / protein phosphorylation / innate immune response / signaling receptor binding / protein kinase binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
Authors | Kim, P.W. / Sun, Z.Y. / Blacklow, S.C. / Wagner, G. / Eck, M.J. | ||||||
Citation | Journal: Science / Year: 2003 Title: A zinc clasp structure tethers Lck to T cell coreceptors CD4 and CD8. Authors: Kim, P.W. / Sun, Z.Y. / Blacklow, S.C. / Wagner, G. / Eck, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q69.cif.gz | 159 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q69.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 1q69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q69_validation.pdf.gz | 351.1 KB | Display | wwPDB validaton report |
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Full document | 1q69_full_validation.pdf.gz | 452.8 KB | Display | |
Data in XML | 1q69_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1q69_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/1q69 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/1q69 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2262.751 Da / Num. of mol.: 1 / Fragment: Human CD8 alpha Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD8A OR MAL / Plasmid: pMM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P01732 |
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#2: Protein/peptide | Mass: 3299.578 Da / Num. of mol.: 1 / Fragment: Human Lck / Mutation: M14L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LCK / Plasmid: pMM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P06239 |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | pH: 5.1 / Pressure: ambient / Temperature: 298 K | |||||||||||||||
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics Software ordinal: 1 Details: The structures are based on a total of 181 distance restraints (176 NOEs, four Zn-S restraints, one hydrogen bond) and 48 angle restraints (42 dihedral angle restraints, six S-Zn-S angle ...Details: The structures are based on a total of 181 distance restraints (176 NOEs, four Zn-S restraints, one hydrogen bond) and 48 angle restraints (42 dihedral angle restraints, six S-Zn-S angle restraints from Cd-H HMQC experiments). | |||||||||||||||
NMR representative | Selection criteria: noe limit 0.5 angstrom, angle violation 5 degrees | |||||||||||||||
NMR ensemble | Conformer selection criteria: The submitted conformer models are the 10 structures with the lowest energy. Conformers calculated total number: 100 / Conformers submitted total number: 10 |