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- PDB-1hkf: The three dimensional structure of NK cell receptor Nkp44, a trig... -

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Basic information

Entry
Database: PDB / ID: 1hkf
TitleThe three dimensional structure of NK cell receptor Nkp44, a triggering partner in natural cytotoxicity
ComponentsNK CELL ACTIVATING RECEPTOR
KeywordsRECEPTOR / NATURAL CYTOTOXICITY RECEPTOR / NKP44 / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


regulation of innate immune response / plasma membrane => GO:0005886 / regulation of immune response / cellular defense response / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / innate immune response / cell surface ...regulation of innate immune response / plasma membrane => GO:0005886 / regulation of immune response / cellular defense response / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / signaling receptor activity / innate immune response / cell surface / signal transduction / plasma membrane
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsPonassi, M. / Cantoni, C. / Biassoni, R. / Conte, R. / Spallarossa, A. / Moretta, A. / Moretta, L. / Bolognesi, M. / Bordo, D.
CitationJournal: Structure / Year: 2003
Title: The Three-Dimensional Structure of the Human Nk Cell Receptor Nkp44, a Triggering Partner in Natural Cytotoxicity
Authors: Cantoni, C. / Ponassi, M. / Biassoni, R. / Conte, R. / Spallarossa, A. / Moretta, A. / Moretta, L. / Bolognesi, M. / Bordo, D.
History
DepositionMar 10, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NK CELL ACTIVATING RECEPTOR


Theoretical massNumber of molelcules
Total (without water)13,9581
Polymers13,9581
Non-polymers00
Water2,108117
1
A: NK CELL ACTIVATING RECEPTOR

A: NK CELL ACTIVATING RECEPTOR


Theoretical massNumber of molelcules
Total (without water)27,9152
Polymers27,9152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.437, 60.437, 197.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein NK CELL ACTIVATING RECEPTOR / NKP44


Mass: 13957.725 Da / Num. of mol.: 1 / Fragment: IG DOMAIN, RESIDUES 19-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4) / References: UniProt: O95944
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS A TRIGGERING RECEPTOR THAT IS INVOLVED IN TUMOR CELL LYSIS BY HUMAN NATURAL KILLER ...THIS PROTEIN IS A TRIGGERING RECEPTOR THAT IS INVOLVED IN TUMOR CELL LYSIS BY HUMAN NATURAL KILLER CELLS. CONTAINS AN IMMUNOGLOBULIN FOLD.

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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: 3 Å3/Da / Density % sol: 67 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 278 K / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.6 mg/mlprotein1drop
230 %(v/v)PEG4001reservoir
30.1 Mammonium acetate1reservoir
40.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9792
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 11487 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 31 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.6
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 5.7 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.21 Å / Num. measured all: 353554 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 2.24 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 5.7

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 --RANDOM
Rwork0.2399 ---
obs0.2399 11487 98.8 %-
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 0 117 981
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.08
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 10 / % reflection obs: 90 %
Refinement
*PLUS
Rfactor Rfree: 0.245 / Rfactor Rwork: 0.239 / Highest resolution: 2.21 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.87

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