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- PDB-1p6f: Structure of the human natural cytotoxicity receptor NKp46 -

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Basic information

Entry
Database: PDB / ID: 1p6f
TitleStructure of the human natural cytotoxicity receptor NKp46
Componentsnatural cytotoxicity triggering receptor 1
KeywordsIMMUNE SYSTEM / Natural cytotoxicity receptor / NKp46 / NK cell receptor / immunoglobulin fold
Function / homology
Function and homology information


regulation of natural killer cell mediated cytotoxicity / immune response-regulating signaling pathway / natural killer cell activation / SWI/SNF complex / cellular defense response / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signal transduction / plasma membrane
Similarity search - Function
: / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsFoster, C.E. / Colonna, M. / Sun, P.D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the human natural killer (NK) cell activating receptor NKp46 reveals structural relationship to other leukocyte receptor complex immunoreceptors.
Authors: Foster, C.E. / Colonna, M. / Sun, P.D.
History
DepositionApr 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: natural cytotoxicity triggering receptor 1


Theoretical massNumber of molelcules
Total (without water)27,4111
Polymers27,4111
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.731, 85.731, 59.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein natural cytotoxicity triggering receptor 1 / NKp46


Mass: 27411.080 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR D1 AND D2 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O76036
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 298 K / pH: 7.2
Details: PEG 2000, MOPS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.20
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
28-11 %PEG20001reservoir
30.1 MMOPS1reservoirpH7.2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.924
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 2.2→19.46 Å / Num. obs: 12472 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 29.3 Å2
Reflection shellResolution: 2.2→2.34 Å / % possible all: 87.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→19.46 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1284 10.3 %RANDOM
Rwork0.207 ---
obs0.207 12472 --
all-12742 --
Displacement parametersBiso mean: 43.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1500 0 0 86 1586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
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→2.34 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.369 204 11.1 %
Rwork0.307 1628 -
obs--87.6 %
Software
*PLUS
Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.47
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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