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- PDB-1q68: Solution structure of T-cell surface glycoprotein CD4 and Proto-o... -

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Basic information

Entry
Database: PDB / ID: 1q68
TitleSolution structure of T-cell surface glycoprotein CD4 and Proto-oncogene tyrosine-protein kinase LCK fragments
Components
  • Proto-oncogene tyrosine-protein kinase LCK
  • T-cell surface glycoprotein CD4
KeywordsMEMBRANE PROTEIN/TRANSFERASE / Peptide-peptide complex / helix-helix interaction / zinc coordination / beta hairpin / MEMBRANE PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / response to methamphetamine hydrochloride / cellular response to ionomycin / regulation of regulatory T cell differentiation ...regulation of lymphocyte activation / positive regulation of leukocyte cell-cell adhesion / CD27 signaling pathway / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / response to methamphetamine hydrochloride / cellular response to ionomycin / regulation of regulatory T cell differentiation / T cell selection / gamma-delta T cell differentiation / positive regulation of gamma-delta T cell differentiation / Fc-gamma receptor signaling pathway / MHC class II protein binding / positive regulation of kinase activity / FLT3 signaling through SRC family kinases / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / protein antigen binding / positive regulation of monocyte differentiation / Alpha-defensins / Nef Mediated CD4 Down-regulation / intracellular zinc ion homeostasis / positive regulation of heterotypic cell-cell adhesion / CD4 receptor binding / Nef and signal transduction / Co-stimulation by CD28 / Interleukin-2 signaling / CD28 dependent Vav1 pathway / regulation of T cell activation / response to vitamin D / peptidyl-tyrosine autophosphorylation / extracellular matrix structural constituent / Other interleukin signaling / Regulation of KIT signaling / leukocyte migration / phospholipase activator activity / Co-inhibition by CTLA4 / T cell receptor complex / enzyme-linked receptor protein signaling pathway / CD8 receptor binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / pericentriolar material / protein serine/threonine phosphatase activity / PECAM1 interactions / positive regulation of protein kinase activity / positive regulation of T cell receptor signaling pathway / hemopoiesis / regulation of calcium ion transport / macrophage differentiation / Generation of second messenger molecules / positive regulation of calcium ion transport into cytosol / immunoglobulin binding / RHOH GTPase cycle / T cell differentiation / immunological synapse / Co-inhibition by PD-1 / CD28 dependent PI3K/Akt signaling / Binding and entry of HIV virion / T cell receptor binding / phosphatidylinositol 3-kinase binding / coreceptor activity / GPVI-mediated activation cascade / phospholipase binding / T cell costimulation / positive regulation of intrinsic apoptotic signaling pathway / phosphotyrosine residue binding / release of sequestered calcium ion into cytosol / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / positive regulation of T cell proliferation / SH2 domain binding / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / protein tyrosine kinase binding / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / Vpu mediated degradation of CD4 / clathrin-coated endocytic vesicle membrane / calcium-mediated signaling / Signaling by SCF-KIT / platelet activation / positive regulation of protein phosphorylation / positive regulation of T cell activation / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell junction / transmembrane signaling receptor activity / DAP12 signaling / MHC class II protein complex binding / response to estradiol / Downstream TCR signaling / PIP3 activates AKT signaling / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / signaling receptor activity
Similarity search - Function
Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin ...Lck, SH3 domain / Tyrosine-protein kinase Lck, SH2 domain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Immunoglobulin / Immunoglobulin domain / : / SH3 domain / SH2 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / Immunoglobulin V-set domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / Tyrosine-protein kinase Lck
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsKim, P.W. / Sun, Z.Y. / Blacklow, S.C. / Wagner, G. / Eck, M.J.
CitationJournal: 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
DepositionAug 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD4
B: Proto-oncogene tyrosine-protein kinase LCK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0593
Polymers7,9932
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100The submitted conformer models are the 10 structures with the lowest energy.
RepresentativeModel #1noe limit 0.5 angstrom, angle violation 5 degrees

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Components

#1: Protein/peptide T-cell surface glycoprotein CD4 / T-cell surface antigen T4/Leu-3


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.) Homo sapiens (human) / Gene: CD4 / Plasmid: pMM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P01730
#2: Protein/peptide Proto-oncogene tyrosine-protein kinase LCK / P56-LCK / LSK / T cell-specific protein-tyrosine kinase


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.) 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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA, HN(CO)CA, HN(CA)CB, HN(CO)CACB, C(CO)NH, H(CCO)NH, (H)CCH TOCSY
12215N-NOESY, 15N-TOCSY
133D2O NOESY, D2O TOCSY
144Cd-H HMQC, Cd-H NOESY-HMQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM CD4-Lck-Zn2+, U-15N,13C; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol95% H2O/5% D2O
20.5 mM CD4-Lck-Zn2+, U-15N; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol95% H2O/5% D2O
30.5 mM CD4-Lck-Zn2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol100% D2O
41.0 mM CD4-Lck-Cd2+; 20 mM acetate, 20 mM NaCl, 0.15% beta-mercaptoethanol100% D2O
Sample conditionspH: 5.1 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
FelixMolecular Simulations Inc.processing
DYANAGuntert, Wuthrichstructure solution
X-PLORBrungerstructure solution
X-PLORBrungerrefinement
RefinementMethod: 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 representativeSelection criteria: noe limit 0.5 angstrom, angle violation 5 degrees
NMR ensembleConformer selection criteria: The submitted conformer models are the 10 structures with the lowest energy.
Conformers calculated total number: 100 / Conformers submitted total number: 10

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