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- PDB-2ptt: Structure of NK cell receptor 2B4 (CD244) bound to its ligand CD48 -

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Basic information

Entry
Database: PDB / ID: 2ptt
TitleStructure of NK cell receptor 2B4 (CD244) bound to its ligand CD48
Components
  • CD48 antigen
  • Natural killer cell receptor 2B4
KeywordsIMMUNE SYSTEM / 2B4 / CD244 / CD48 / NK cell receptor
Function / homology
Function and homology information


natural killer cell activation involved in immune response / myeloid dendritic cell activation / Cell surface interactions at the vascular wall / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of natural killer cell proliferation / T cell activation / adaptive immune response / membrane raft / external side of plasma membrane / signal transduction / extracellular region
Similarity search - Function
Natural killer cell receptor 2B4, immunoglobulin domain / Natural killer cell receptor 2B4 / : / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Natural killer cell receptor 2B4, immunoglobulin domain / Natural killer cell receptor 2B4 / : / Immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CD48 antigen / Natural killer cell receptor 2B4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD48 antigen
B: Natural killer cell receptor 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5643
Polymers25,4682
Non-polymers961
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.938, 37.270, 94.740
Angle α, β, γ (deg.)90.00, 108.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-112-

HOH

21B-114-

HOH

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Components

#1: Protein CD48 antigen / MRC OX-45 surface antigen / BCM1 surface antigen / BLAST-1 / HM48-1 / sgp-60


Mass: 12940.734 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type1, D1, 2B4-binding domain / Mutation: T34Y, K52R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/6 / Gene: Cd48, Bcm-1 / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P18181
#2: Protein Natural killer cell receptor 2B4 / NKR2B4 / NK cell type I receptor protein 2B4 / CD244 antigen / Non MHC restricted killing associated


Mass: 12526.927 Da / Num. of mol.: 1 / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q07763
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M ammonium sulfate, 0.1 mM MES, 10% dioxane, pH 6.5, 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: Jun 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 28061 / % possible obs: 99.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 53.6
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 8 / Num. unique all: 2733 / % possible all: 97.4

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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 1HNG

1hng


Resolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.712 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24365 1413 5 %RANDOM
Rwork0.19012 ---
obs0.19279 26647 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.428 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0.37 Å2
2--1.5 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.63→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1723 0 5 213 1941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221765
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.9542388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0115209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.34524.76786
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66415322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.353159
X-RAY DIFFRACTIONr_chiral_restr0.1420.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2684
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21190
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4451.51076
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31821710
X-RAY DIFFRACTIONr_scbond_it3.3973786
X-RAY DIFFRACTIONr_scangle_it5.1854.5678
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.631→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 115 -
Rwork0.208 1897 -
obs--97.29 %

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