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- PDB-6ewa: Crystal structure of HLA-A2 in complex with LILRB1 -

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Basic information

Entry
Database: PDB / ID: 6ewa
TitleCrystal structure of HLA-A2 in complex with LILRB1
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • LIR-1
  • Polyprotein
KeywordsIMMUNE SYSTEM / LILRB1 / peptide-MHC complex / HLA-A2 / peptide conformation / crystallisation chaperone
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 / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity ...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 / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / negative regulation of serotonin secretion / 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 / negative regulation of transforming growth factor beta production / negative regulation of cytokine production involved in immune response / negative regulation of alpha-beta T cell activation / dendritic cell differentiation / protein phosphatase 1 binding / interleukin-10-mediated signaling pathway / 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 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 / integrase activity / negative regulation of natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / positive regulation of macrophage cytokine production / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / Minus-strand DNA synthesis / Plus-strand DNA synthesis / 2-LTR circle formation / Uncoating of the HIV Virion / CD8 receptor binding / Vpr-mediated nuclear import of PICs / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of calcium ion transport / Early Phase of HIV Life Cycle / beta-2-microglobulin binding / MHC class I protein binding / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / endoplasmic reticulum exit site / negative regulation of cell cycle / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of type II interferon production / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of tumor necrosis factor production / telomerase activity / 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 / Binding and entry of HIV virion / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / viral life cycle / SH2 domain binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / Assembly Of The HIV Virion / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Budding and maturation of HIV virion / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / HIV-1 retropepsin / peptide antigen assembly with MHC class II protein complex / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / RNA-directed DNA polymerase activity / MHC class II protein complex / negative regulation of forebrain neuron differentiation / exoribonuclease H activity / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 ...: / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / MHC classes I/II-like antigen recognition protein / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / : / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LIR-1 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Gag-Pol polyprotein / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1 / Polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
Model details================CATEGORY 5: Authors of Structure============================ Enter authors of the ...================CATEGORY 5: Authors of Structure============================ Enter authors of the deposited structures (e.g. Surname, F.M.)
AuthorsStones, D.H. / Willcox, B.E. / Mohammed, F.
CitationJournal: J. Immunol. Methods / Year: 2019
Title: Application of the immunoregulatory receptor LILRB1 as a crystallisation chaperone for human class I MHC complexes.
Authors: Mohammed, F. / Stones, D.H. / Willcox, B.E.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Polyprotein
D: LIR-1
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
G: Polyprotein
H: LIR-1


Theoretical massNumber of molelcules
Total (without water)132,8808
Polymers132,8808
Non-polymers00
Water81145
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Polyprotein
D: LIR-1


Theoretical massNumber of molelcules
Total (without water)66,4404
Polymers66,4404
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
G: Polyprotein
H: LIR-1


Theoretical massNumber of molelcules
Total (without water)66,4404
Polymers66,4404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.150, 116.150, 192.820
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P61769
#3: Protein/peptide Polyprotein


Mass: 993.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9WGX1, UniProt: P04585*PLUS
#4: Protein LIR-1


Mass: 21747.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: D9IDM8, UniProt: Q8NHL6*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 17.5% PEG 3350, 0.2M Ammonium acetate, 0.1M Tris HCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2006
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.39→48.679 Å / Num. obs: 60013 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.042 / Rrim(I) all: 0.13 / Rsym value: 0.122 / Net I/av σ(I): 5.2 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.39-2.529.50.5371.485050.1820.5670.53797.7
2.52-2.679.80.451.682070.1520.4750.45100
2.67-2.869.80.3322.377200.1110.350.332100
2.86-3.099.80.223.572330.0730.2320.22100
3.09-3.389.80.1465.166570.0490.1550.146100
3.38-3.789.40.1334.760750.0460.1410.133100
3.78-4.379.40.0837.253610.0290.0880.083100
4.37-5.359.50.04813.345730.0160.050.048100
5.35-7.569.70.0421636010.0140.0450.042100
7.56-48.6798.90.03117.420810.0110.0330.03199.6

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Processing

Software
NameVersionClassification
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P7Q

1p7q


Resolution: 2.39→44.59 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.881 / SU B: 9.434 / SU ML: 0.214 / SU R Cruickshank DPI: 0.3572 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.268
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3020 5 %RANDOM
Rwork0.2281 ---
obs0.2306 56936 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.82 Å2 / Biso mean: 35.594 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.02 Å2-0 Å2
2---0.03 Å20 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.39→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9104 0 0 45 9149
Biso mean---24.63 -
Num. residues----1123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199089
X-RAY DIFFRACTIONr_bond_other_d0.0020.028101
X-RAY DIFFRACTIONr_angle_refined_deg1.2641.92812395
X-RAY DIFFRACTIONr_angle_other_deg0.919318573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95123.162427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.587151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.211562
X-RAY DIFFRACTIONr_chiral_restr0.0770.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110331
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022203
LS refinement shellResolution: 2.392→2.454 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 211 -
Rwork0.295 4033 -
all-4244 -
obs--96.04 %

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