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- PDB-2esv: Structure of the HLA-E-VMAPRTLIL/KK50.4 TCR complex -

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Basic information

Entry
Database: PDB / ID: 2esv
TitleStructure 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
KeywordsIMMUNE SYSTEM / T cell receptor / TCR / HLA-E / CMV / pMHC-TCR complex
Function / homology
Function and homology information


symbiont-mediated suppression 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 lectin-like receptor binding / natural killer cell tolerance induction ...symbiont-mediated suppression 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 lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / 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 / negative regulation of natural killer cell mediated cytotoxicity / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / T cell receptor binding / negative regulation of T cell proliferation / : / : / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / Downstream TCR signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis
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 / MHC class I alpha chain, alpha1 alpha2 domains ...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 / Immunoglobulin-like fold / Immunoglobulins / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsHoare, H.L. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2006
Title: Structural basis for a major histocompatibility complex class Ib-restricted T cell response
Authors: Hoare, H.L. / Sullivan, L.C. / Pietra, G. / Clements, C.S. / Lee, E.J. / Ely, L.K. / Beddoe, T. / Falco, M. / Kjer-Nielsen, L. / Reid, H.H. / McCluskey, J. / Moretta, L. / Rossjohn, J. / Brooks, A.G.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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, alpha chain E
B: Beta-2-microglobulin
P: VMAPRTLIL peptide from CMV gpUL40
D: KK50.4 T cell receptor alpha chain
E: KK50.4 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,89910
Polymers94,2655
Non-polymers6355
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.096, 41.462, 112.471
Angle α, β, γ (deg.)90.00, 114.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, alpha chain E / HLA-E*103 / MHC class I antigen E


Mass: 31867.098 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide VMAPRTLIL peptide from CMV gpUL40 / HLA-Cw3 leader sequence fragment


Mass: 1014.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: de novo peptide synthesis / References: UniProt: P16780*PLUS

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KK50.4 T cell receptor ... , 2 types, 2 molecules DE

#4: Protein KK50.4 T cell receptor alpha chain


Mass: 22221.713 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01848
#5: Protein KK50.4 T cell receptor beta chain


Mass: 27282.391 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01850

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Non-polymers , 2 types, 190 molecules

#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 19-22% PEG 3350, 0.2M Potassium Iodide, pH 6.9-7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. obs: 67491
Reflection shellHighest 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
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1467 5 %RANDOM
Rwork0.214 ---
all0.218 ---
obs0.218 29119 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.311 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.83 Å2
2---0.05 Å20 Å2
3----0.56 Å2
Refine analyzeLuzzati coordinate error obs: 0.46 Å / Luzzati sigma a obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 5 185 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216768
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9369202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49323.902346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.518151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4431548
X-RAY DIFFRACTIONr_chiral_restr0.070.2975
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025280
X-RAY DIFFRACTIONr_nbd_refined0.1840.22823
X-RAY DIFFRACTIONr_nbtor_refined0.30.24463
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2317
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.29
X-RAY DIFFRACTIONr_mcbond_it0.8734105
X-RAY DIFFRACTIONr_mcangle_it1.65456625
X-RAY DIFFRACTIONr_scbond_it2.45872955
X-RAY DIFFRACTIONr_scangle_it3.965102577
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.454 102 -
Rwork0.339 1850 -
all-1952 -
obs--87.18 %

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