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- PDB-1z2k: NMR structure of the D1 domain of the Natural Killer Cell Recepto... -

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Basic information

Entry
Database: PDB / ID: 1z2k
TitleNMR structure of the D1 domain of the Natural Killer Cell Receptor, 2B4
ComponentsNatural killer cell receptor 2B4
KeywordsIMMUNE SYSTEM / Immunoglobulin motif / beta sandwich / V-domain / Natural Killer Cell Receptor
Function / homology
Function and homology information


myeloid dendritic cell activation / natural killer cell activation involved in immune response / Cell surface interactions at the vascular wall / positive regulation of natural killer cell proliferation / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / adaptive immune response / external side of plasma membrane / innate immune response
Similarity search - Function
Natural killer cell receptor 2B4, immunoglobulin domain / Natural killer cell receptor 2B4 / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Natural killer cell receptor 2B4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsAmes, J.B. / Vyas, V. / Lusin, J.D. / Mariuzza, R.
CitationJournal: Biochemistry / Year: 2005
Title: NMR Structure of the Natural Killer Cell Receptor 2B4: Implications for Ligand Recognition
Authors: Ames, J.B. / Vyas, V. / Lusin, J.D. / Mariuzza, R.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: 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_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)12,2111
Polymers12,2111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 25structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #7closest to the average

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Components

#1: Protein Natural killer cell receptor 2B4 / NKR2B4 / NK cell type I receptor protein 2B4 / CD244 antigen / Non MHC restricted killing associated


Mass: 12210.551 Da / Num. of mol.: 1 / Fragment: D1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd244, 2b4, Nmrk / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07763

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D NOESY
NMR detailsText: The structure was determinded using standard 2D homonuclear NOESY and 3D heteronuclear techniques

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Sample preparation

DetailsContents: 0.5mM 2B4 D1 domain, U-15N,13C; 50 mM phosphate buffer; pH 7.2; 90% H2O, 10% D2O
Solvent system: aqueous solution at 298 degrees Kelvin
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
XwinNMR2.5Brukercollection
X-PLOR3.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 2657 restraints, 2359 are NOE-derived distance constraints, 128 dihedral angle restraints, 170 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 25 / Conformers submitted total number: 14

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