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- PDB-4no0: Crystal structure of non-phosphorylated form of RQA_V phosphopept... -

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Basic information

Entry
Database: PDB / ID: 4no0
TitleCrystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Lymphocyte-specific protein 1
KeywordsIMMUNE SYSTEM/ANTIGEN / Nonphosphorylated peptide / peptide-MHC complex / MHC / LILRB1 / post translational modification / peptide conformation / tumor immunology / tumor antigen / neoepitope / IMMUNE SYSTEM-ANTIGEN complex
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 / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / 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 / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / Fc receptor mediated inhibitory signaling pathway / MHC class Ib protein binding / MHC class Ib receptor activity / immune response-regulating signaling pathway / 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 serotonin secretion / negative regulation of cytokine production involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of mononuclear cell proliferation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / cellular response to interleukin-7 / positive regulation of macrophage cytokine production / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of interleukin-10 production / CD8 receptor binding / MHC class I protein binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / negative regulation of calcium ion transport / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / TAP binding / negative regulation of cell cycle / protection from natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / positive regulation of defense response to virus by host / SH2 domain binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / response to virus / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / receptor internalization / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence
Similarity search - Function
Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / : / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / : / 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 / : / 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 / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Lymphocyte-specific protein 1 / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMohammed, F. / Stones, D.H. / Willcox, B.E.
CitationJournal: Oncotarget / Year: 2017
Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Lymphocyte-specific protein 1
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8115
Polymers66,7494
Non-polymers621
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-14 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.300, 117.300, 96.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 3 types, 3 molecules ABD

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / Class I histocompatibility antigen A*0201


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-300)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769
#4: 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: 21747.340 Da / Num. of mol.: 1 / Fragment: UNP residues 27-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILT2, LILRB1, LIR1, MIR7 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8NHL6

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Lymphocyte-specific protein 1 / 47 kDa actin-binding protein / 52 kDa phosphoprotein / pp52 / Lymphocyte-specific antigen WP34


Mass: 1302.520 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 249-260) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P33241

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Non-polymers , 2 types, 49 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsIN LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 1, L68P, I142T, AND S155I ARE NATURAL VARIANTS

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG3350, 0.1 M HEPES, pH 7.4, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.7→29.325 Å / Num. obs: 21132 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 36 % / Biso Wilson estimate: 47.502 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 33.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.7-2.80.8166.22786012171199.5
2.8-2.90.628.02686281861199.4
2.9-30.5319.13609601652199.3
3-3.30.30215.161399613782198.9
3.3-3.50.18924.08688211857199.4
3.5-40.11537.731175653187198.6
4-50.07259.261161343173198.4
5-60.06265.18520651428199.3
6-100.05472.87565351575199.4
10-29.3250.04293.4914553446193.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7Q

1p7q


Resolution: 2.7→29.325 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.851 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.2236 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7445 / SU B: 15.83 / SU ML: 0.315 / SU R Cruickshank DPI: 0.6386 / SU Rfree: 0.4092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.639 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3094 1080 5.1 %RANDOM
Rwork0.2688 ---
obs0.2709 20054 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.38 Å2 / Biso mean: 54.8343 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 4 48 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214700
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9346410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68123.407226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20915691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2871532
X-RAY DIFFRACTIONr_chiral_restr0.1010.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213707
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 79 -
Rwork0.436 1463 -
all-1542 -
obs--99.68 %

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