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- PDB-6ewo: Crystal structure of non-phosphorylated form of RTF PHOSPHOPEPTID... -

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Basic information

Entry
Database: PDB / ID: 6ewo
TitleCrystal structure of non-phosphorylated form of RTF PHOSPHOPEPTIDE BOUND TO HLA-A2 in complex with LILRB1
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • LIR-1
  • Synemin
KeywordsIMMUNE SYSTEM / LILRB1 / NONPHOSPHOPEPTIDE / peptide-MHC complex / HLA-A2 / tumour antigen / crystallisation chaperone
Function / homology
Function and homology information


fast-twitch skeletal muscle fiber contraction / intermediate filament binding / neurofilament cytoskeleton / 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 ...fast-twitch skeletal muscle fiber contraction / intermediate filament binding / neurofilament cytoskeleton / 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 / negative regulation of transforming growth factor beta production / MHC class I receptor activity / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / dendritic cell differentiation / intermediate filament cytoskeleton organization / 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 / vinculin binding / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of dendritic cell apoptotic process / costamere / negative regulation of interferon-beta production / intermediate filament cytoskeleton / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / intermediate filament / structural constituent of muscle / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of macrophage cytokine production / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / 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 / adherens junction / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / sarcolemma / 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
Similarity search - Function
Synemin / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / : / Immunoglobulin domain / Immunoglobulin ...Synemin / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / : / 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
LIR-1 / Synemin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 6, 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: Synemin
D: LIR-1
E: HLA class I histocompatibility antigen, A-2 alpha chain
F: Beta-2-microglobulin
G: Synemin
H: LIR-1


Theoretical massNumber of molelcules
Total (without water)132,9788
Polymers132,9788
Non-polymers00
Water4,089227
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Synemin
D: LIR-1


Theoretical massNumber of molelcules
Total (without water)66,4894
Polymers66,4894
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: Synemin
H: LIR-1


Theoretical massNumber of molelcules
Total (without water)66,4894
Polymers66,4894
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.300, 116.300, 192.600
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 Synemin / Desmuslin


Mass: 1042.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMMERCIAL SYNTHESIS / Source: (synth.) Homo sapiens (human) / References: UniProt: O15061
#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.: 227 / 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: 56.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M Potassium sodium tartrate

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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: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.3→19.7 Å / Num. obs: 66969 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.331 % / Biso Wilson estimate: 38.572 Å2 / Rmerge F obs: 0.113 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.105 / Χ2: 0.876 / Net I/σ(I): 23.61 / Num. measured all: 758810 / Scaling rejects: 103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.45.5380.6730.7342.8241698800875290.80794
2.4-2.511.380.3660.6075.0876803675367490.63599.9
2.5-2.611.990.290.4886.4169374578757860.509100
2.6-2.712.0970.2330.3917.7860026496249620.408100
2.7-2.812.1410.1860.3049.4651891427442740.317100
2.8-2.912.2180.1550.25410.845794374837480.265100
2.9-312.2610.1390.21911.9639603323032300.229100
3-412.2580.0560.09326.8321554917588175850.097100
4-512.2770.020.03659.9477874634463430.037100
5-612.1510.0180.03463.9834413283328320.035100
6-1011.8460.0160.02972.237136313631350.03100
10-19.710.8660.0110.0288.8886499387960.02184.9

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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: 2.3→19.7 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.051 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3266 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.249
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 3401 5.1 %RANDOM
Rwork0.2321 ---
obs0.2344 63567 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.52 Å2 / Biso mean: 37.859 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.3→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9135 0 0 227 9362
Biso mean---30.99 -
Num. residues----1126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199416
X-RAY DIFFRACTIONr_bond_other_d0.0020.028453
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9312804
X-RAY DIFFRACTIONr_angle_other_deg0.914319449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73751120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81523.036471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.788151466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2841578
X-RAY DIFFRACTIONr_chiral_restr0.0810.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022322
LS refinement shellResolution: 2.303→2.362 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 235 -
Rwork0.306 4381 -
all-4616 -
obs--94.88 %

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