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- PDB-6ewc: Crystal structure of non-phosphorylated form of RLS PHOSPHOPEPTID... -

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Entry
Database: PDB / ID: 6ewc
TitleCrystal structure of non-phosphorylated form of RLS 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
  • Reticulophagy regulator 2
KeywordsIMMUNE SYSTEM / LILRB1 / NONPHOSPHOPEPTIDE / peptide-MHC complex / HLA-A2 / tumour antigen / crystallisation chaperone
Function / homology
Function and homology information


endoplasmic reticulum-autophagosome adaptor activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / 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 ...endoplasmic reticulum-autophagosome adaptor activity / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / 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 receptor activity / MHC class Ib protein binding / 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 alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of osteoclast development / 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 interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / endoplasmic reticulum organization / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / reticulophagy / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / negative regulation of calcium ion transport / endoplasmic reticulum exit site / negative regulation of cell cycle / MHC class I protein binding / negative regulation of type II interferon production / TAP binding / collagen catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / 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 / 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / receptor internalization / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to virus / specific granule lumen / positive regulation of type II interferon production
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 ...: / : / 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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Reticulophagy regulator 2 / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 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.)
AuthorsMohammed, F. / Stones, D.H. / Willcox, B.E.
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 / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.3Nov 6, 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: Reticulophagy regulator 2
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
G: Reticulophagy regulator 2
H: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)133,0088
Polymers133,0088
Non-polymers00
Water00
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Reticulophagy regulator 2
D: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)66,5044
Polymers66,5044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-24 kcal/mol
Surface area27780 Å2
MethodPISA
2
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
G: Reticulophagy regulator 2
H: Leukocyte immunoglobulin-like receptor subfamily B member 1


Theoretical massNumber of molelcules
Total (without water)66,5044
Polymers66,5044
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-25 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.500, 117.500, 203.700
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 Reticulophagy regulator 2


Mass: 1057.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMMERCIAL SYNTHESIS / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NC44
#4: Protein Leukocyte immunoglobulin-like receptor subfamily B member 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: 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12.8% PEG 3350, 3% Tacsimate, 10% dimethyl sulphoxide

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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: Mar 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 3.2→19.58 Å / Num. obs: 26415 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.669 % / Biso Wilson estimate: 15.902 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.173 / Rrim(I) all: 0.191 / Χ2: 0.887 / Net I/σ(I): 10.73 / Num. measured all: 149740 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.2-3.35.5480.4423.8912971237123380.880.48998.6
3.3-3.45.5740.4014.3611588210820790.8730.44498.6
3.4-3.55.6130.3235.4210514188918730.9140.35699.2
3.5-45.5920.2197.8237793686767590.9630.24198.4
4-4.55.6610.13612.3322961415740560.9860.14997.6
4.5-55.7130.10115.4714752268225820.9910.11196.3
5-65.7760.11314.0516798307429080.9910.12594.6
6-105.860.09716.1218032335530770.9940.10791.7
10-19.585.8290.04729.36433110137430.9980.05273.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1p7q


Resolution: 3.2→19.58 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.838 / SU B: 22.608 / SU ML: 0.369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.486
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1276 4.8 %RANDOM
Rwork0.2056 ---
obs0.2076 25137 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 96.64 Å2 / Biso mean: 29.616 Å2 / Biso min: 13.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å2-0 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 3.2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9226 0 0 0 9226
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199308
X-RAY DIFFRACTIONr_bond_other_d0.0040.028318
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.92912682
X-RAY DIFFRACTIONr_angle_other_deg1.028319100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59451124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26623.156450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.085151388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5341568
X-RAY DIFFRACTIONr_chiral_restr0.0690.21326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110596
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022280
LS refinement shellResolution: 3.2→3.281 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 94 -
Rwork0.287 1824 -
all-1918 -
obs--98.61 %

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