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- PDB-3p2t: Crystal Structure of Leukocyte Ig-like Receptor LILRB4 (ILT3/LIR-... -

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Basic information

Entry
Database: PDB / ID: 3p2t
TitleCrystal Structure of Leukocyte Ig-like Receptor LILRB4 (ILT3/LIR-5/CD85k)
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 4
KeywordsIMMUNE SYSTEM / LILR / IG / Inhibitory receptor / disulfide
Function / homology
Function and homology information


transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production ...transmembrane receptor protein tyrosine kinase inhibitor activity / negative regulation of cytotoxic T cell differentiation / negative regulation of IP-10 production / negative regulation of T cell costimulation / tolerance induction / negative regulation of protein tyrosine kinase activity / inhibitory MHC class I receptor activity / Fc receptor mediated inhibitory signaling pathway / negative regulation of T cell cytokine production / negative regulation of interleukin-5 production / negative regulation of signaling receptor activity / positive regulation of CD8-positive, alpha-beta T cell differentiation / negative regulation of monocyte activation / immune response-regulating signaling pathway / interleukin-10-mediated signaling pathway / positive regulation of T cell anergy / negative regulation of chemokine production / protein tyrosine kinase inhibitor activity / signaling receptor inhibitor activity / negative regulation of protein localization to nucleus / positive regulation of regulatory T cell differentiation / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of osteoclast differentiation / negative regulation of interleukin-6 production / negative regulation of type II interferon production / fibronectin binding / negative regulation of tumor necrosis factor production / apolipoprotein binding / negative regulation of MAPK cascade / negative regulation of canonical NF-kappaB signal transduction / negative regulation of T cell proliferation / negative regulation of cytokine production involved in inflammatory response / negative regulation of miRNA transcription / cytokine-mediated signaling pathway / receptor internalization / cytoplasmic side of plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein phosphatase binding / adaptive immune response / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte immunoglobulin-like receptor subfamily B member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsChen, Y. / Nam, G. / Cheng, H. / Zhang, J.H. / Willcox, B.E. / Gao, G.F.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Crystal structure of leukocyte Ig-like receptor LILRB4 (ILT3/LIR-5/CD85k): a myeloid inhibitory receptor involved in immune tolerance
Authors: Cheng, H. / Mohammed, F. / Nam, G. / Chen, Y. / Qi, J. / Garner, L.I. / Allen, R.L. / Yan, J. / Willcox, B.E. / Gao, G.F.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0754
Polymers21,7871
Non-polymers2883
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Leukocyte immunoglobulin-like receptor subfamily B member 4
hetero molecules

A: Leukocyte immunoglobulin-like receptor subfamily B member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1508
Polymers43,5732
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2610 Å2
ΔGint-14 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.863, 61.863, 115.826
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

21A-415-

HOH

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 4 / LILRB4 (ILT3/LIR-5/CD85k) / Leukocyte immunoglobulin-like receptor 5 / LIR-5 / Immunoglobulin-like ...LILRB4 (ILT3/LIR-5/CD85k) / Leukocyte immunoglobulin-like receptor 5 / LIR-5 / Immunoglobulin-like transcript 3 / ILT-3 / Monocyte inhibitory receptor HM18 / CD85 antigen-like family member K


Mass: 21786.658 Da / Num. of mol.: 1 / Fragment: residues in UNP 24-219 / Mutation: I133C, H143C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB4, ILT3, LIR5 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NHJ6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M sodium sulfate heptahydrate, 20%(w/v) polyethylene glycol 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 30, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.699→50 Å / Num. obs: 25152 / % possible obs: 98.2 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2D3V

2d3v


Resolution: 1.699→22.488 Å / SU ML: 0.16 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1262 5.08 %RANDOM
Rwork0.1857 ---
obs0.1873 24860 97.35 %-
all-24860 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.46 Å2 / ksol: 0.389 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1926 Å20 Å2-0 Å2
2--1.1926 Å20 Å2
3----2.3852 Å2
Refinement stepCycle: LAST / Resolution: 1.699→22.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 15 234 1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041599
X-RAY DIFFRACTIONf_angle_d0.9432180
X-RAY DIFFRACTIONf_dihedral_angle_d17.475584
X-RAY DIFFRACTIONf_chiral_restr0.07229
X-RAY DIFFRACTIONf_plane_restr0.005280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.76740.21161330.17062503X-RAY DIFFRACTION94
1.7674-1.84780.21061380.16762588X-RAY DIFFRACTION98
1.8478-1.94510.23241370.16832606X-RAY DIFFRACTION99
1.9451-2.06690.23381580.17012605X-RAY DIFFRACTION99
2.0669-2.22640.181360.17032647X-RAY DIFFRACTION99
2.2264-2.45020.22681270.1772638X-RAY DIFFRACTION99
2.4502-2.80420.24621460.19232663X-RAY DIFFRACTION99
2.8042-3.53080.20771380.17682665X-RAY DIFFRACTION97
3.5308-22.49030.19971490.18852683X-RAY DIFFRACTION93

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