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- PDB-2ptu: Structure of NK cell receptor 2B4 (CD244) -

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Basic information

Entry
Database: PDB / ID: 2ptu
TitleStructure of NK cell receptor 2B4 (CD244)
ComponentsNatural killer cell receptor 2B4CD244
KeywordsIMMUNE SYSTEM / 2B4 / CD244 / NK cell receptor
Function / homology
Function and homology information


positive regulation of granzyme B production / myeloid dendritic cell activation / natural killer cell activation involved in immune response / Cell surface interactions at the vascular wall / positive regulation of inositol phosphate biosynthetic process / positive regulation of natural killer cell proliferation / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / positive regulation of interleukin-8 production / positive regulation of type II interferon production ...positive regulation of granzyme B production / myeloid dendritic cell activation / natural killer cell activation involved in immune response / Cell surface interactions at the vascular wall / positive regulation of inositol phosphate biosynthetic process / positive regulation of natural killer cell proliferation / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / positive regulation of interleukin-8 production / positive regulation of type II interferon production / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDeng, L. / Velikovsky, C.A. / Mariuzza, R.A.
CitationJournal: Immunity / Year: 2007
Title: Structure of natural killer receptor 2B4 bound to CD48 reveals basis for heterophilic recognition in signaling lymphocyte activation molecule family.
Authors: Velikovsky, C.A. / Deng, L. / Chlewicki, L.K. / Fernandez, M.M. / Kumar, V. / Mariuzza, R.A.
History
DepositionMay 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Natural killer cell receptor 2B4
B: Natural killer cell receptor 2B4
C: Natural killer cell receptor 2B4
D: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)50,1084
Polymers50,1084
Non-polymers00
Water2,306128
1
A: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)12,5271
Polymers12,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)12,5271
Polymers12,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)12,5271
Polymers12,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Natural killer cell receptor 2B4


Theoretical massNumber of molelcules
Total (without water)12,5271
Polymers12,5271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.040, 183.268, 59.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is one of the monomers in the asymmetric unit.

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Components

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


Mass: 12526.927 Da / Num. of mol.: 4 / Fragment: Ig-like 1, D1, CD48-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Cd244, 2b4, Nmrk / Plasmid: pT7.7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q07763
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M ammonium dihydrogen phosphate, 0.1 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 57316 / % possible obs: 85.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 50.5 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.9
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4034 / % possible all: 60

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTT

2ptt


Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.767 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26947 1658 5 %RANDOM
Rwork0.22477 ---
obs0.22711 31285 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.35 Å2
Baniso -1Baniso -2Baniso -3
1-4.19 Å20 Å20 Å2
2---1.79 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 0 128 3435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9434572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.22925.949158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.68615589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.242157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022539
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.21280
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22150
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9851.52121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78623339
X-RAY DIFFRACTIONr_scbond_it2.09231470
X-RAY DIFFRACTIONr_scangle_it3.3454.51233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.381→2.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 104 -
Rwork0.28 1804 -
obs--74.13 %

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