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- PDB-2otp: Crystal Structure of Immunoglobulin-Like Transcript 1 (ILT1/LIR7/... -

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Basic information

Entry
Database: PDB / ID: 2otp
TitleCrystal Structure of Immunoglobulin-Like Transcript 1 (ILT1/LIR7/LILRA2)
ComponentsLeukocyte immunoglobulin-like receptor subfamily A member 2
KeywordsIMMUNE SYSTEM / ILT1 / activating receptor / dimer / monomer / domain swapping
Function / homology
Function and homology information


innate immune response activating cell surface receptor signaling pathway / granulocyte macrophage colony-stimulating factor production / granulocyte colony-stimulating factor production / interleukin-6 production / interleukin-8 production / positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / IgM binding / negative regulation of toll-like receptor 4 signaling pathway / neutrophil activation involved in immune response ...innate immune response activating cell surface receptor signaling pathway / granulocyte macrophage colony-stimulating factor production / granulocyte colony-stimulating factor production / interleukin-6 production / interleukin-8 production / positive regulation of cell activation / positive regulation of tumor necrosis factor production => GO:0032760 / IgM binding / negative regulation of toll-like receptor 4 signaling pathway / neutrophil activation involved in immune response / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of calcium ion transport / plasma membrane => GO:0005886 / positive regulation of interleukin-1 beta production / antigen binding / defense response / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / signaling receptor activity / innate immune response / signal transduction / extracellular region
Similarity search - Function
Alpha-1B-glycoprotein/leukocyte immunoglobulin-like receptor / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Alpha-1B-glycoprotein/leukocyte immunoglobulin-like receptor / 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 A member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO / Resolution: 2.6 Å
AuthorsGao, F. / Peng, H. / Chen, Y. / Liu, Y. / Gao, G.F.
CitationJournal: To be Published
Title: Crystal Structure of 3D Domain Swapped Dimer of Immunoglobulin-Like Transcript 1 (ILT1/LIR7/LILRA2), Molecular Insight into Group 1 Activating Receptor Forming Unique MW Interaction Pattern
Authors: Chen, Y. / Gao, F. / Peng, H. / Liu, Y. / Gao, G.F.
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocyte immunoglobulin-like receptor subfamily A member 2
B: Leukocyte immunoglobulin-like receptor subfamily A member 2


Theoretical massNumber of molelcules
Total (without water)43,8192
Polymers43,8192
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-72 kcal/mol
Surface area20970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.842, 72.971, 131.853
Angle α, β, γ (deg.)90.00, 90.32, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-218-

HOH

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily A member 2 / Leukocyte immunoglobulin-like receptor 7 / LIR-7 / Immunoglobulin- like transcript 1 / ILT-1 / ...Leukocyte immunoglobulin-like receptor 7 / LIR-7 / Immunoglobulin- like transcript 1 / ILT-1 / CD85h antigen / LILRA2


Mass: 21909.473 Da / Num. of mol.: 2 / Fragment: D1D2, Ig-like C2-type / Mutation: R142C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRA2, ILT1, LIR7 / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8N149
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 126

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.6M MgSO4, 0.1M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→44.21 Å / Num. obs: 11930 / Redundancy: 6.68 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.1
Reflection shellResolution: 2.5→2.74 Å / Redundancy: 7.08 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 2.6→30 Å / Num. parameters: 28188 / Num. restraintsaints: 36735 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?; THIS IS A TWINNED DATA. THE TWINNING OPERATOR IS (H,K,L) -> (-h, -k, l) AND THE TWINNING FRACTION IS 0.377.
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 --RANDOM
Rwork0.1761 ---
all0.1765 11343 --
obs0.1765 11313 92.2 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3131.5
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 0 66 3128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0153
X-RAY DIFFRACTIONs_zero_chiral_vol0.027
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.085
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.044
X-RAY DIFFRACTIONs_approx_iso_adps0.043

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