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- PDB-4ll9: Crystal structure of D3D4 domain of the LILRB1 molecule -

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Basic information

Entry
Database: PDB / ID: 4ll9
TitleCrystal structure of D3D4 domain of the LILRB1 molecule
ComponentsLeukocyte immunoglobulin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / Ig-like domain / immune-modulatory molecule
Function / homology
Function and homology information


HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / negative regulation of serotonin secretion / dendritic cell differentiation / protein phosphatase 1 binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of interferon-beta production / negative regulation of endocytosis / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / T cell proliferation involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-10 production / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / MHC class I protein binding / positive regulation of defense response to virus by host / negative regulation of T cell proliferation / SH2 domain binding / response to virus / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / defense response to virus / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / 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
IODIDE ION / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.686 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

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leukocyte immunoglobulin-like receptor subfamily B member 1
B: Leukocyte immunoglobulin-like receptor subfamily B member 1
C: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,52415
Polymers64,0013
Non-polymers1,52312
Water1,62190
1
A: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9686
Polymers21,3341
Non-polymers6355
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8415
Polymers21,3341
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7144
Polymers21,3341
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.257, 71.976, 75.036
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-204-

IOD

21B-321-

HOH

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Components

#1: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1 / LIR-1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / ...LIR-1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7


Mass: 21333.711 Da / Num. of mol.: 3 / Fragment: D3D4 domain, UNP residues 222-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NHL6
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2M NaI, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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 12, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.686→50 Å / Num. all: 18041 / Num. obs: 17596 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.04 Å2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.686→32.808 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7378 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 32.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2748 889 5.05 %RANDOM
Rwork0.2448 16701 --
obs0.2464 17590 97.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.31 Å2 / Biso mean: 70.1278 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: LAST / Resolution: 2.686→32.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 12 90 4590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054616
X-RAY DIFFRACTIONf_angle_d1.2396282
X-RAY DIFFRACTIONf_chiral_restr0.043665
X-RAY DIFFRACTIONf_plane_restr0.007834
X-RAY DIFFRACTIONf_dihedral_angle_d16.7341680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6862-2.85440.37351360.33152664280095
2.8544-3.07460.34921450.32212790293597
3.0746-3.38380.35181340.28022775290997
3.3838-3.87270.28321640.24692791295598
3.8727-4.87670.24091500.20082825297598
4.8767-32.81060.23721600.22992856301698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1942.2827-1.20645.7713-0.53894.8626-0.53620.2339-0.7057-0.61440.3315-0.62530.61310.12150.22230.37160.01140.10860.328-0.04260.3083-11.0277-24.9937-17.2445
23.8258-1.4536-1.3977.5896-5.23092.0033-0.09560.0239-1.2585-0.69080.51330.76122.0044-1.13420.91140.6443-0.14590.10690.41950.05921.2152-14.2671-37.0163-19.46
33.3476-0.3455-0.4097.16380.15456.2894-0.41280.238-0.5489-0.08760.2702-0.83420.82270.32140.10410.36790.01850.14940.4693-0.03580.4907-8.1571-25.9907-16.7779
42.8375-0.74471.00112.0433-0.9343.70030.07490.310.3573-0.1593-0.17620.2729-1.1361-1.38930.11820.60060.32680.03730.70760.04950.3927-23.2915-0.0062-19.3214
55.57547.0964-0.0189.4647-1.57195.03910.5562-0.2705-2.1712-0.867-0.7881-1.8866-0.2486-0.1112-0.02370.70070.3880.07180.74090.17640.6989-19.0313-6.7699-25.743
63.128-0.43461.21322.3756-0.00923.583-0.14860.1533-0.2365-0.07690.1114-0.0746-0.5812-0.66360.08050.43940.18360.08350.47710.09880.3496-22.5952-0.012-20.5077
76.0951-0.47622.67991.4889-0.75737.7344-0.24130.5550.0338-0.14760.21760.3064-0.2053-0.1306-0.24030.2825-0.02790.02960.2789-0.02430.4048-43.7573.16852.6695
85.6576-0.18751.21581.4097-0.31722.3286-0.1988-0.1772-0.0685-0.08570.07120.1114-0.19870.1387-0.00070.42880.00570.01160.26-0.02130.2232-27.2681-0.88965.2064
95.25343.9896-2.06014.8376-0.61964.3294-0.16860.2728-0.0732-0.49540.09490.2267-0.04620.17570.23510.37630.0429-0.01850.3111-0.00840.267-15.7776-1.17474.5426
104.15990.68980.39823.4522-1.16370.70790.13540.67660.2485-0.1669-0.1306-0.4282-0.94840.0134-0.18150.84190.02260.01240.47680.11560.4073-8.08779.807229.0561
114.6963-1.12542.48197.16660.55673.06540.81961.0521.69180.1068-0.1537-1.28280.3204-0.458-0.31851.01930.1429-0.05170.5030.14470.5406-4.835916.776930.8594
124.03350.4729-1.33632.8928-1.00475.2155-0.26830.18660.1797-0.44050.12760.51340.3009-0.1546-0.06050.45680.1275-0.07560.35880.04590.1741-18.35690.506130.6268
133.94950.24950.88348.11080.27358.51160.00640.194-0.1008-0.6494-0.1137-0.05380.9242-0.55970.13450.5712-0.0061-0.03150.47290.02860.3019-24.1135-9.414128.3687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2:46 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 47:58 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 59:93 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 94:140 )
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 141:150 )
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 151:197 )
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 2:58 )
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 59:139 )
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 140:197 )
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 2:39 )
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 40:58 )
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 59:133 )
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 134:197 )

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