- PDB-2esv: Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex -
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Basic information
Entry
Database: PDB / ID: 2esv
Title
Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex
Components
(KK50.4 T cell receptor ...) x 2
Beta-2-microglobulin
HLA class I histocompatibility antigen, alpha chain E
VMAPRTLIL peptide from CMV gpUL40
Keywords
IMMUNE SYSTEM / T cell receptor / TCR / HLA-E / CMV / pMHC-TCR complex
Function / homology
Function and homology information
suppression by virus of host natural killer cell activation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding ...suppression by virus of host natural killer cell activation / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / alpha-beta T cell receptor complex / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / 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 / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / MHC class I protein binding / alpha-beta T cell activation / Generation of second messenger molecules / protection from natural killer cell mediated cytotoxicity / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / response to bacterium / 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 / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / Downstream TCR signaling / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation Similarity search - Function
Herpesvirus UL40 / Glycoprotein of human cytomegalovirus HHV-5 / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 ...Herpesvirus UL40 / Glycoprotein of human cytomegalovirus HHV-5 / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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 / : / 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 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
IODIDE ION / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, alpha chain E / Protein UL40 / Beta-2-microglobulin Similarity search - Component
Biological species
Homo sapiens (human)
Method
X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Highest resolution: 2.6 Å / Num. obs: 67491
Reflection shell
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 11.2 / Num. unique all: 29161
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PDB_EXTRACT
1.7
dataextraction
HKL-2000
datareduction
SCALEPACK
datascaling
AMoRE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.6→36.4 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.859 / SU B: 25.202 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.046 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.292
1467
5 %
RANDOM
Rwork
0.214
-
-
-
all
0.218
-
-
-
obs
0.218
29119
93.74 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.311 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.07 Å2
0 Å2
-0.83 Å2
2-
-
-0.05 Å2
0 Å2
3-
-
-
-0.56 Å2
Refine analyze
Luzzati coordinate error obs: 0.46 Å / Luzzati sigma a obs: 0.56 Å
Refinement step
Cycle: LAST / Resolution: 2.6→36.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6587
0
5
185
6777
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.006
0.021
6768
X-RAY DIFFRACTION
r_angle_refined_deg
1.016
1.936
9202
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.561
5
810
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.493
23.902
346
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.518
15
1105
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.443
15
48
X-RAY DIFFRACTION
r_chiral_restr
0.07
0.2
975
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
5280
X-RAY DIFFRACTION
r_nbd_refined
0.184
0.2
2823
X-RAY DIFFRACTION
r_nbtor_refined
0.3
0.2
4463
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.124
0.2
317
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.174
0.2
51
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.154
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
0.87
3
4105
X-RAY DIFFRACTION
r_mcangle_it
1.654
5
6625
X-RAY DIFFRACTION
r_scbond_it
2.458
7
2955
X-RAY DIFFRACTION
r_scangle_it
3.965
10
2577
LS refinement shell
Resolution: 2.6→2.668 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.454
102
-
Rwork
0.339
1850
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all
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1952
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obs
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87.18 %
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