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- PDB-6aee: Crystal structure of the four Ig-like domains of LILRB1 complexed... -

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Basic information

Entry
Database: PDB / ID: 6aee
TitleCrystal structure of the four Ig-like domains of LILRB1 complexed with HLA-G
Components
  • 9 Mer Peptide (RL9) From Histone H2A.x
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain G
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
KeywordsIMMUNE SYSTEM / leukocyte immunoglobulin-like receptor / immunotherapy
Function / homology
Function and homology information


peripheral B cell tolerance induction / positive regulation of tolerance induction / 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 / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway ...peripheral B cell tolerance induction / positive regulation of tolerance induction / 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 / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / positive regulation of natural killer cell cytokine production / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / cis-Golgi network membrane / negative regulation of transforming growth factor beta production / interleukin-10-mediated signaling pathway / negative regulation of immune response / negative regulation of cytokine production involved in immune response / negative regulation of alpha-beta T cell activation / positive regulation of T cell tolerance induction / negative regulation of serotonin secretion / dendritic cell differentiation / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of G0 to G1 transition / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / positive regulation of regulatory T cell differentiation / positive regulation of macrophage cytokine production / CD8 receptor binding / negative regulation of interleukin-10 production / protein homotrimerization / MHC class I protein binding / negative regulation of calcium ion transport / negative regulation of type II interferon production / T cell proliferation involved in immune response / negative regulation of cell cycle / protection from natural killer cell mediated cytotoxicity / negative regulation of tumor necrosis factor production / positive regulation of endothelial cell apoptotic process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / positive regulation of interleukin-12 production / Inhibition of DNA recombination at telomere / Meiotic synapsis / RNA Polymerase I Promoter Opening / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Assembly of the ORC complex at the origin of replication / SH2 domain binding / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / : / : / Condensation of Prophase Chromosomes / negative regulation of angiogenesis / positive regulation of receptor binding / Chromatin modifications during the maternal to zygotic transition (MZT) / early endosome lumen / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA Polymerase I Promoter Escape / peptide antigen assembly with MHC class II protein complex / Transcriptional regulation by small RNAs / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Histone H2A conserved site / Histone H2A signature. / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Histone H2A conserved site / Histone H2A signature. / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leukocyte immunoglobulin like receptor B1 / Histone H2A type 1-B/E / HLA class I histocompatibility antigen, alpha chain G / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.303 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 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: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: 9 Mer Peptide (RL9) From Histone H2A.x
D: HLA class I histocompatibility antigen, alpha chain G
E: Beta-2-microglobulin
F: 9 Mer Peptide (RL9) From Histone H2A.x
G: Leukocyte immunoglobulin-like receptor subfamily B member 1
H: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)178,4358
Polymers178,4358
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, alpha chain G
B: Beta-2-microglobulin
C: 9 Mer Peptide (RL9) From Histone H2A.x
G: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)89,2174
Polymers89,2174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: HLA class I histocompatibility antigen, alpha chain G
E: Beta-2-microglobulin
F: 9 Mer Peptide (RL9) From Histone H2A.x
H: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)89,2174
Polymers89,2174
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.683, 154.681, 98.198
Angle α, β, γ (deg.)90.00, 102.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain G / HLA G antigen / MHC class I antigen G


Mass: 32046.559 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300 / Mutation: C42S, L110I, Q115R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-G / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P17693
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide 9 Mer Peptide (RL9) From Histone H2A.x


Mass: 1148.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04908*PLUS
#4: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1


Mass: 44143.148 Da / Num. of mol.: 2 / Fragment: UNP residues 25-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Production host: Trichoplusia ni (cabbage looper) / Variant (production host): Hi5 / References: UniProt: A0A0G2JQ44, UniProt: Q8NHL6*PLUS
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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M imidazole malate, 15%(w/v) PEG4000, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 29866 / % possible obs: 99.9 % / Redundancy: 4.2 % / CC1/2: 0.972 / Rpim(I) all: 0.105 / Net I/σ(I): 7.89
Reflection shellResolution: 3.3→3.42 Å / Num. unique obs: 2993

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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: 2DYP, 4LL9

2dyp

4ll9


Resolution: 3.303→45.42 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2665 1509 5.05 %
Rwork0.2203 --
obs0.2227 29866 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.303→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12038 0 0 0 12038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212382
X-RAY DIFFRACTIONf_angle_d0.63116831
X-RAY DIFFRACTIONf_dihedral_angle_d6.6937357
X-RAY DIFFRACTIONf_chiral_restr0.0411742
X-RAY DIFFRACTIONf_plane_restr0.0042201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3029-3.40950.32051100.27432077X-RAY DIFFRACTION79
3.4095-3.53130.33121110.25522584X-RAY DIFFRACTION97
3.5313-3.67260.30321380.24752640X-RAY DIFFRACTION100
3.6726-3.83970.3311380.23892610X-RAY DIFFRACTION100
3.8397-4.0420.25931290.22452627X-RAY DIFFRACTION100
4.042-4.29510.27121430.20672627X-RAY DIFFRACTION100
4.2951-4.62640.25571340.19592644X-RAY DIFFRACTION100
4.6264-5.09140.22241630.19372617X-RAY DIFFRACTION100
5.0914-5.82690.2681570.21372610X-RAY DIFFRACTION100
5.8269-7.33620.28291300.23362658X-RAY DIFFRACTION100
7.3362-45.4240.22791560.21032663X-RAY DIFFRACTION100

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