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- PDB-1ugn: Crystal structure of LIR1.02, one of the alleles of LIR1 -

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Entry
Database: PDB / ID: 1ugn
TitleCrystal structure of LIR1.02, one of the alleles of LIR1
ComponentsLeukocyte immunoglobulin-like receptor 1
KeywordsIMMUNE SYSTEM / immunoglobulin-like folds
Function / homology
Function and homology information


HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / negative regulation of serotonin secretion / dendritic cell differentiation / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / T cell proliferation involved in immune response / MHC class I protein binding / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / SH2 domain binding / response to virus / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / defense response to virus / adaptive immune response / cellular response to lipopolysaccharide / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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
Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShiroishi, M. / Rasubala, L. / Kuroki, K. / Amano, K. / Tsuchiya, N. / Tokunaga, K. / Kohda, D. / Maenaka, K.
CitationJournal: Hum.Mol.Genet. / Year: 2005
Title: Extensive polymorphisms of LILRB1 (ILT2, LIR1) and their association with HLA-DRB1 shared epitope negative rheumatoid arthritis.
Authors: Kuroki, K. / Tsuchiya, N. / Shiroishi, M. / Rasubala, L. / Yamashita, Y. / Matsuta, K. / Fukazawa, T. / Kusaoi, M. / Murakami, Y. / Takiguchi, M. / Juji, T. / Hashimoto, H. / Kohda, D. / ...Authors: Kuroki, K. / Tsuchiya, N. / Shiroishi, M. / Rasubala, L. / Yamashita, Y. / Matsuta, K. / Fukazawa, T. / Kusaoi, M. / Murakami, Y. / Takiguchi, M. / Juji, T. / Hashimoto, H. / Kohda, D. / Maenaka, K. / Tokunaga, K.
History
DepositionJun 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte immunoglobulin-like receptor 1


Theoretical massNumber of molelcules
Total (without water)22,0861
Polymers22,0861
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.437, 103.414, 53.022
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Leukocyte immunoglobulin-like receptor 1 / LIR1


Mass: 22085.723 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (domain1 and 2) / Mutation: A70T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NHL6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.18 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris chloride, 0.7M potassium sodium tartrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 18378 / % possible obs: 95.9 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1539 / % possible all: 83.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UFU

1ufu


Resolution: 1.8→8 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 922 -random
Rwork0.205 ---
obs0.205 18080 95.4 %-
Displacement parametersBiso mean: 21.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 0 175 1639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.005
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.318 136 -
Rwork0.256 --
obs-2394 81.3 %

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