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- PDB-1q68: Solution structure of T-cell surface glycoprotein CD4 and Proto-o... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q68 | ||||||
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Title | Solution structure of T-cell surface glycoprotein CD4 and Proto-oncogene tyrosine-protein kinase LCK fragments | ||||||
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![]() | MEMBRANE PROTEIN/TRANSFERASE / Peptide-peptide complex / helix-helix interaction / zinc coordination / beta hairpin / MEMBRANE PROTEIN-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / Fc-gamma receptor signaling pathway / T cell selection / MHC class II protein binding / CD28 co-stimulation ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / Fc-gamma receptor signaling pathway / T cell selection / MHC class II protein binding / CD28 co-stimulation / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / intracellular zinc ion homeostasis / FLT3 signaling through SRC family kinases / positive regulation of monocyte differentiation / CD4 receptor binding / Nef Mediated CD4 Down-regulation / Alpha-defensins / positive regulation of kinase activity / Nef and signal transduction / positive regulation of heterotypic cell-cell adhesion / Interleukin-2 signaling / CD28 dependent Vav1 pathway / regulation of T cell activation / T cell receptor complex / extracellular matrix structural constituent / Regulation of KIT signaling / Other interleukin signaling / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / leukocyte migration / phospholipase activator activity / enzyme-linked receptor protein signaling pathway / 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 / PECAM1 interactions / CD28 dependent PI3K/Akt signaling / regulation of calcium ion transport / phospholipase binding / RHOH GTPase cycle / macrophage differentiation / hemopoiesis / Generation of second messenger molecules / immunological synapse / T cell differentiation / PD-1 signaling / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / phosphatidylinositol 3-kinase binding / T cell receptor binding / positive regulation of calcium-mediated signaling / 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 / positive regulation of interleukin-2 production / phosphotyrosine residue binding / SH2 domain binding / protein tyrosine kinase binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Vpu mediated degradation of CD4 / calcium-mediated signaling / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / clathrin-coated endocytic vesicle membrane / Signaling by SCF-KIT / platelet activation / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / PIP3 activates AKT signaling / DAP12 signaling / MHC class II protein complex binding / Clathrin-mediated endocytosis / virus receptor activity / signaling receptor activity / T cell receptor signaling pathway / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein phosphatase binding / protein tyrosine kinase activity / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics | ||||||
![]() | Kim, P.W. / Sun, Z.Y. / Blacklow, S.C. / Wagner, G. / Eck, M.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 226.2 KB | Display | ![]() |
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PDB format | ![]() | 185.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 356.1 KB | Display | ![]() |
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Full document | ![]() | 471.3 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 20.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein/peptide | Mass: 4693.604 Da / Num. of mol.: 1 / Fragment: residues 421-458 / Mutation: M407L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 3299.578 Da / Num. of mol.: 1 / Fragment: residues 6-34 / Mutation: M14L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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Sample preparation
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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 419 distance restraints (406 NOEs, four Zn-S restraints from Cd-H HMQC experiments, nine hydrogen bonds) and 63 angle restraints (57 dihedral angle ...Details: The structures are based on a total of 419 distance restraints (406 NOEs, four Zn-S restraints from Cd-H HMQC experiments, nine hydrogen bonds) and 63 angle restraints (57 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 |