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- PDB-1vdg: Crystal structure of LIR1.01, one of the alleles of LIR1 -

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Basic information

Entry
Database: PDB / ID: 1vdg
TitleCrystal structure of LIR1.01, one of the alleles of LIR1
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / immunoglobulin-like
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 / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / 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 / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / 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 / negative regulation of natural killer cell mediated cytotoxicity / dendritic cell differentiation / negative regulation of mononuclear cell proliferation / 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 / 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 / T cell proliferation involved in immune response / 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 / cellular response to lipopolysaccharide / defense response to virus / adaptive immune response / 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: 2.8 Å
AuthorsShiroishi, M. / Rasubala, L. / Kuroki, K. / Amano, K. / Tsuchiya, N. / Tokunaga, K. / Kohda, D. / Maenaka, K.
CitationJournal: To be Published
Title: Crystal structure of LIR1.03, one of the alleles of LIR1
Authors: Shiroishi, M. / Rasubala, L. / Kuroki, K. / Amano, K. / Tsuchiya, N. / Tokunaga, K. / Kohda, D. / Maenaka, K.
History
DepositionMar 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: Leukocyte immunoglobulin-like receptor subfamily B member 1
B: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)44,0012
Polymers44,0012
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.969, 93.220, 57.773
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1 / Leukocyte immunoglobulin-like receptor 1 / LIR-1 / Immunoglobulin- like transcript 2 / ILT-2 / ...Leukocyte immunoglobulin-like receptor 1 / LIR-1 / Immunoglobulin- like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7 / CD85j antigen


Mass: 22000.662 Da / Num. of mol.: 2 / Fragment: Ligand binding domain (domain 1 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


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris chloride, 0.7M potassium sodium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 10575 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 9
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.545 / Num. unique all: 1007 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UGN

1ugn


Resolution: 2.8→19.98 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 867342.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 519 5.1 %RANDOM
Rwork0.241 ---
obs0.25 10088 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.3155 Å2 / ksol: 0.358498 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 0 61 3010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.212
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.782.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 83 5 %
Rwork0.328 1573 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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