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- PDB-1efx: STRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL RECE... -

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Basic information

Entry
Database: PDB / ID: 1efx
TitleSTRUCTURE OF A COMPLEX BETWEEN THE HUMAN NATURAL KILLER CELL RECEPTOR KIR2DL2 AND A CLASS I MHC LIGAND HLA-CW3
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA-CW3 (HEAVY CHAIN)
  • NATURAL KILLER CELL RECEPTOR KIR2DL2
  • PEPTIDE FROM IMPORTIN ALPHA-2
KeywordsIMMUNE SYSTEM / MHC / HLA / class I / KIR / NK cell receptor / Immunoglobulin fold / receptor-MHC complex
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / host cell / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding ...Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / host cell / nuclear import signal receptor activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear localization sequence binding / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / ISG15 antiviral mechanism / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / protein import into nucleus / cellular response to nicotine / histone deacetylase binding / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / nuclear membrane / Estrogen-dependent gene expression / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity
Similarity search - Function
Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats ...Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Immunoglobulin / Immunoglobulin domain / 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 / Armadillo-like helical / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / HLA class I histocompatibility antigen, C alpha chain / Killer cell immunoglobulin-like receptor 2DL2 / Importin subunit alpha-1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBoyington, J.C. / Motyka, S.A. / Schuck, P. / Brooks, A.G. / Sun, P.D.
Citation
Journal: Nature / Year: 2000
Title: Crystal structure of an NK cell immunoglobulin-like receptor in complex with its class I MHC ligand.
Authors: Boyington, J.C. / Motyka, S.A. / Schuck, P. / Brooks, A.G. / Sun, P.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal Structure of the HLA-Cw3 Allotype-specific Killer Cell Inhibitory Receptor KIR2DL2
Authors: Snyder, G.A. / Brooks, A.G. / Sun, P.D.
History
DepositionFeb 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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
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: HLA-CW3 (HEAVY CHAIN)
B: BETA-2-MICROGLOBULIN
C: PEPTIDE FROM IMPORTIN ALPHA-2
D: NATURAL KILLER CELL RECEPTOR KIR2DL2
E: NATURAL KILLER CELL RECEPTOR KIR2DL2


Theoretical massNumber of molelcules
Total (without water)89,0345
Polymers89,0345
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.540, 90.330, 207.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the 1:1 complex between KIR2DL2 and HLA-Cw3 observed in the asymmetric unit The biological assembly is the 1:1 complex between KIR2DL2 and HLA-Cw3 observed in the asymmetric unit

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Components

#1: Protein HLA-CW3 (HEAVY CHAIN)


Mass: 32185.391 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR ALPHA-1, ALPHA-2 AND ALPHA-3 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: MODIFIED PET30A / Production host: Escherichia coli (E. coli) / References: GenBank: 495038, UniProt: P10321*PLUS
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MATURE FORM / Source: (gene. exp.) Homo sapiens (human) / Plasmid: MODIFIED PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide PEPTIDE FROM IMPORTIN ALPHA-2 /


Mass: 868.029 Da / Num. of mol.: 1 / Fragment: RESIDUES 204-212 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence is naturally found in homo sapiens (human).
References: UniProt: P52292
#4: Protein NATURAL KILLER CELL RECEPTOR KIR2DL2


Mass: 22050.682 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR D1 AND D2 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: MODIFIED PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P43627
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.64 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, calcium chloride, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
26 %PEG200001reservoir
350 mM1reservoirCaCl2
450 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.0358
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0358 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 25779 / Num. obs: 24517 / % possible obs: 92.1 % / Observed criterion σ(I): -0.5 / Redundancy: 4.2 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.6
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 2 / Num. unique all: 2321 / % possible all: 75.4
Reflection shell
*PLUS
% possible obs: 75.4 % / Num. unique obs: 1976

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: KIR2DL2 (PDB ENTRY 2DL2) and HLA-A2 (PDB ENTRY 1B0G)

2dl2

1b0g


Resolution: 3→10 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2163178.14 / Data cutoff high rms absF: 2163178.14 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1085 4.8 %Random
Rwork0.231 ---
all0.212 23289 --
obs0.209 22800 88.5 %-
Solvent computationSolvent model: flat model / Bsol: 42.0521 Å2 / ksol: 0.28471 e/Å3
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1-12.6 Å20 Å20 Å2
2--15.3 Å20 Å2
3----27.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6226 0 0 185 6411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.456 134 4.6 %
Rwork0.394 2788 -
obs--69.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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