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- PDB-4lla: Crystal structure of D3D4 domain of the LILRB2 molecule -

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Basic information

Entry
Database: PDB / ID: 4lla
TitleCrystal structure of D3D4 domain of the LILRB2 molecule
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 2
KeywordsIMMUNE SYSTEM / Ig-like domain / immune-modulatory molecule
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 / positive regulation of T cell tolerance induction / interleukin-10-mediated signaling pathway / protein phosphatase 1 binding / positive regulation of regulatory T cell differentiation / regulation of dendritic cell differentiation / heterotypic cell-cell adhesion / regulation of long-term synaptic potentiation / 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 / negative regulation of T cell proliferation / positive regulation of T cell proliferation / : / cell adhesion molecule binding / 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 / Immunoglobulins / Immunoglobulin-like fold / 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 / SAD / Resolution: 2.502 Å
AuthorsNam, G. / Shi, Y. / Ryu, M. / Wang, Q. / Song, H. / Liu, J. / Yan, J. / Qi, J. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2013
Title: Crystal structures of the two membrane-proximal Ig-like domains (D3D4) of LILRB1/B2: alternative models for their involvement in peptide-HLA binding
Authors: Nam, G. / Shi, Y. / Ryu, M. / Wang, Q. / Song, H. / Liu, J. / Yan, J. / Qi, J. / Gao, G.F.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references

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Structure visualization

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MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,5673
Polymers64,5673
Non-polymers00
Water1,26170
1
A: Leukocyte immunoglobulin-like receptor subfamily B member 2


Theoretical massNumber of molelcules
Total (without water)21,5221
Polymers21,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukocyte immunoglobulin-like receptor subfamily B member 2


Theoretical massNumber of molelcules
Total (without water)21,5221
Polymers21,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukocyte immunoglobulin-like receptor subfamily B member 2


Theoretical massNumber of molelcules
Total (without water)21,5221
Polymers21,5221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.367, 66.170, 83.719
Angle α, β, γ (deg.)90.00, 95.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 2 / LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / ...LIR-2 / Leukocyte immunoglobulin-like receptor 2 / CD85 antigen-like family member D / Immunoglobulin-like transcript 4 / ILT-4 / Monocyte/macrophage immunoglobulin-like receptor 10 / MIR-10


Mass: 21522.230 Da / Num. of mol.: 3 / Mutation: D3D4 domain, UNP residues 222-419
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO NATURAL VARIANT RS386056.

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 3.5M sodium formate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 20, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 21731 / Num. obs: 21660 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 49.65 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.502→43.247 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7372 / SU ML: 0.37 / σ(F): 1.33 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 1106 5.11 %RANDOM
Rwork0.2213 ---
all0.2239 21645 --
obs0.2239 21645 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.21 Å2 / Biso mean: 51.6463 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: LAST / Resolution: 2.502→43.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 0 70 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074668
X-RAY DIFFRACTIONf_angle_d1.3116354
X-RAY DIFFRACTIONf_chiral_restr0.07690
X-RAY DIFFRACTIONf_plane_restr0.01843
X-RAY DIFFRACTIONf_dihedral_angle_d18.3421734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5017-2.61550.3711240.30982532265698
2.6155-2.75340.37751420.305525222664100
2.7534-2.92580.37591410.299425572698100
2.9258-3.15170.35761500.282625592709100
3.1517-3.46870.33021340.244225802714100
3.4687-3.97040.24331400.220425582698100
3.9704-5.0010.21471470.17342577272499
5.001-43.25330.21311280.18072654278299
Refinement TLS params.Method: refined / Origin x: 28.028 Å / Origin y: 9.663 Å / Origin z: 20.7969 Å
111213212223313233
T0.2031 Å20.0047 Å2-0.0152 Å2-0.1842 Å2-0.0076 Å2--0.1719 Å2
L0.1943 °20.0283 °2-0.0499 °2-0.0801 °2-0.082 °2---0.0286 °2
S-0.0281 Å °-0.0593 Å °0.0344 Å °-0.0125 Å °-0.0192 Å °0.0232 Å °0.0458 Å °0.0382 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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