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- PDB-6aed: Crystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/... -

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Basic information

Entry
Database: PDB / ID: 6aed
TitleCrystal Structure of the four Ig-like domain of LILRB2(LIR2/ILT4/CD85d)
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 2
KeywordsIMMUNE SYSTEM / leukocyte immunoglobulin-like receptor
Function / homology
Function and homology information


negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / 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 ...negative regulation of antigen processing and presentation / negative regulation of postsynaptic density organization / 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 / immune response-regulating signaling pathway / interleukin-10-mediated signaling pathway / positive regulation of T cell tolerance induction / protein phosphatase 1 binding / regulation of dendritic cell differentiation / regulation of long-term synaptic potentiation / heterotypic cell-cell adhesion / positive regulation of regulatory T cell differentiation / negative regulation of protein metabolic process / MHC class I protein binding / negative regulation of calcium ion transport / tertiary granule membrane / ficolin-1-rich granule membrane / cellular defense response / positive regulation of T cell proliferation / cell adhesion molecule binding / negative regulation of T cell proliferation / 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 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-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte immunoglobulin-like receptor subfamily B member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.797 Å
AuthorsWang, Q. / Song, H. / Qi, J. / Gao, G.F.
CitationJournal: Cell. Mol. Immunol. / Year: 2019
Title: Structures of the four Ig-like domain LILRB2 and the four-domain LILRB1 and HLA-G1 complex.
Authors: Wang, Q. / Song, H. / Cheng, H. / Qi, J. / Nam, G. / Tan, S. / Wang, J. / Fang, M. / Shi, Y. / Tian, Z. / Cao, X. / An, Z. / Yan, J. / Gao, G.F.
History
DepositionAug 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 23, 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 2


Theoretical massNumber of molelcules
Total (without water)43,5791
Polymers43,5791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20210 Å2
Unit cell
Length a, b, c (Å)172.196, 172.196, 65.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2


Mass: 43579.008 Da / Num. of mol.: 1 / Fragment: UNP residues 27-419 / Mutation: V213M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB2 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi5 / References: UniProt: Q8N423
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: 6.44 Å3/Da / Density % sol: 80.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8.5, 25%(v/v) tert-butanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.797→50 Å / Num. obs: 11011 / % possible obs: 99.9 % / Redundancy: 9.8 % / Net I/σ(I): 16.83
Reflection shellResolution: 3.8→3.94 Å / Num. unique obs: 1114

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GW5, 4LLA

2gw5

4lla


Resolution: 3.797→42.752 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.78
RfactorNum. reflection% reflection
Rfree0.2873 521 4.73 %
Rwork0.2639 --
obs0.2651 11011 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.797→42.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 0 0 2983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033074
X-RAY DIFFRACTIONf_angle_d0.7024200
X-RAY DIFFRACTIONf_dihedral_angle_d12.9661139
X-RAY DIFFRACTIONf_chiral_restr0.045455
X-RAY DIFFRACTIONf_plane_restr0.005547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7971-4.1790.35011210.31552489X-RAY DIFFRACTION94
4.179-4.7830.2721310.24232644X-RAY DIFFRACTION100
4.783-6.02340.28571350.25472662X-RAY DIFFRACTION100
6.0234-42.75450.2591340.25532695X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 4.076 Å / Origin y: -65.0019 Å / Origin z: 5.175 Å
111213212223313233
T-0.1078 Å2-0.1089 Å2-0.2124 Å2-0.3229 Å20.0033 Å2--0.0636 Å2
L0.0363 °20.0092 °20.0498 °2--0.0208 °20.0351 °2--0.0467 °2
S-0.0674 Å °-0.0325 Å °0.0904 Å °-0.029 Å °0.0412 Å °0.0361 Å °-0.2336 Å °0.0355 Å °0.0016 Å °
Refinement TLS groupSelection details: all

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