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- PDB-1p1z: X-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RE... -

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Basic information

Entry
Database: PDB / ID: 1p1z
TitleX-RAY CRYSTAL STRUCTURE OF THE LECTIN-LIKE NATURAL KILLER CELL RECEPTOR LY-49C BOUND TO ITS MHC CLASS I LIGAND H-2Kb
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • LY49-C antigen
  • Ovalbumin peptide
KeywordsIMMUNE SYSTEM / NK / Kb / MHC / Antigenic Peptide / Ly49 / OVA
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / response to steroid hormone / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / response to corticosterone / antigen processing and presentation of exogenous peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / inner ear development / cellular defense response / phagocytic vesicle / monoatomic ion transport / Neutrophil degranulation / response to progesterone / early endosome lumen / Neutrophil degranulation / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to estrogen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / carbohydrate binding / protein refolding / cellular response to lipopolysaccharide / protease binding / vesicle / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / cell adhesion / defense response to bacterium / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle / external side of plasma membrane / innate immune response / lysosomal membrane / calcium ion binding / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Ly49-like, N-terminal / : / Ly49-like protein, N-terminal region / Natural killer cell receptor-like, C-type lectin-like domain / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Ovalbumin / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Killer cell lectin-like receptor 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.26 Å
AuthorsDimasi, N. / Natarajan, K. / Rangjin, G. / Dam, J. / Margulies, D.H. / Mariuzza, R.A.
CitationJournal: Nat.Immunol. / Year: 2003
Title: Variable MHC class I engagement by Ly49 natural killer cell receptors demonstrated by the crystal structure of Ly49C bound to H-2K(b).
Authors: Dam, J. / Guan, R. / Natarajan, K. / Dimasi, N. / Chlewicki, L.K. / Kranz, D.M. / Schuck, P. / Margulies, D.H. / Mariuzza, R.A.
History
DepositionApr 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: Ovalbumin peptide
D: LY49-C antigen


Theoretical massNumber of molelcules
Total (without water)58,6874
Polymers58,6874
Non-polymers00
Water00
1
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: Ovalbumin peptide
D: LY49-C antigen

A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: Ovalbumin peptide
D: LY49-C antigen


Theoretical massNumber of molelcules
Total (without water)117,3738
Polymers117,3738
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)149.047, 149.047, 64.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 31648.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide Ovalbumin peptide


Mass: 964.137 Da / Num. of mol.: 1 / Fragment: residues 257-264 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Gallus gallus (chicken).
References: UniProt: P01012
#4: Protein LY49-C antigen / Killer cell lectin-like receptor 3 / T-cell surface glycoprotein LY-49C / LY49-C antigen / ...Killer cell lectin-like receptor 3 / T-cell surface glycoprotein LY-49C / LY49-C antigen / Lymphocyte antigen 49C / 5E6


Mass: 14369.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KLRA3 OR LY49C OR LY-49C / Production host: Escherichia coli (E. coli) / References: UniProt: Q64329
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: 3.05 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% PEG 20000, 2% DIOXANE, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18-10 mg/mlprotein1drop
210 %(w/v)PEG200001reservoir
32 %(v/v)dioxane1reservoir
40.1 Mbicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.26→50 Å / Num. all: 32168 / Num. obs: 32168 / % possible obs: 99.5 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 3.2 / Rmerge(I) obs: 0.096
Reflection shellResolution: 3.26→3.28 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.31 / % possible all: 99.6
Reflection
*PLUS
Num. obs: 12168
Reflection shell
*PLUS
Lowest resolution: 3.31 Å / % possible obs: 99.8 % / Num. unique obs: 596 / Rmerge(I) obs: 0.264

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.26→50 Å / σ(F): 2.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3156 588 RANDOM
Rwork0.2625 --
all-11803 -
obs-11153 -
Refinement stepCycle: LAST / Resolution: 3.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 0 0 0 3926
Refinement
*PLUS
Num. reflection obs: 11771 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.014
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.52

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