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- PDB-2gw5: Crystal Structure of LIR-2 (ILT4) at 1.8 : differences from LIR-1... -

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Basic information

Entry
Database: PDB / ID: 2gw5
TitleCrystal Structure of LIR-2 (ILT4) at 1.8 : differences from LIR-1 (ILT2) in regions implicated in the binding of the Cytomegalovirus class I MHC homolog UL18
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 2 precursor
KeywordsIMMUNE SYSTEM / Ig like domains
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding ...negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / interleukin-10-mediated signaling pathway / negative regulation of T cell costimulation / positive regulation of tolerance induction / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / positive regulation of long-term synaptic depression / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / positive regulation of regulatory T cell differentiation / regulation of dendritic cell differentiation / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / negative regulation of protein metabolic process / MHC class I protein binding / tertiary granule membrane / negative regulation of calcium ion transport / ficolin-1-rich granule membrane / cellular defense response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of protein dephosphorylation / cell adhesion molecule binding / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell signaling / amyloid-beta binding / cellular response to lipopolysaccharide / adaptive immune response / learning or memory / cell surface receptor signaling pathway / immune response / Neutrophil degranulation / protein-containing complex binding / cell surface / signal transduction / protein homodimerization activity / extracellular space / membrane / 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
ISOPROPYL ALCOHOL / Leukocyte immunoglobulin-like receptor subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWillcox, B.E. / Thomas, L.M. / Chapman, T.L. / Heikema, A.P. / West, A.P. / Bjorkman, P.J.
CitationJournal: Bmc Struct.Biol. / Year: 2002
Title: Crystal structure of LIR-2 (ILT4) at 1.8 A: differences from LIR-1 (ILT2) in regions implicated in the binding of the Human Cytomegalovirus class I MHC homolog UL18.
Authors: Willcox, B.E. / Thomas, L.M. / Chapman, T.L. / Heikema, A.P. / West, A.P. / Bjorkman, P.J.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type

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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 2 precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9952
Polymers21,9351
Non-polymers601
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.530, 62.530, 106.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2 precursor / Leukocyte immunoglobulin-like receptor 2 / LIR-2 / Immunoglobulin- like transcript 4 / ILT-4 / ...Leukocyte immunoglobulin-like receptor 2 / LIR-2 / Immunoglobulin- like transcript 4 / ILT-4 / Monocyte/macrophage immunoglobulin-like receptor 10 / MIR-10 / CD85d antigen


Mass: 21934.693 Da / Num. of mol.: 1 / Fragment: N-terminal Domains 1 and 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N423
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 10% Isopropanol, 20% PEG 4000 streak seeded., VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2001
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→34.1 Å / Num. all: 20290 / Num. obs: 19241 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.83 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G0X

1g0x


Resolution: 1.8→34.08 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.2 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27864 991 4.9 %RANDOM
Rwork0.24041 ---
obs0.2423 19239 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.611 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 4 145 1547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.9681989
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2625184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9622.36455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95415209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3171510
X-RAY DIFFRACTIONr_chiral_restr0.1610.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3140.2656
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2945
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6231.5962
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45121491
X-RAY DIFFRACTIONr_scbond_it3.8653595
X-RAY DIFFRACTIONr_scangle_it5.3624.5496
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 89 -
Rwork0.294 1398 -
obs--100 %

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