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- PDB-6g9q: Ternary complex of P14 TCR with murine MHC class I H-2 Db in comp... -

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Basic information

Entry
Database: PDB / ID: 6g9q
TitleTernary complex of P14 TCR with murine MHC class I H-2 Db in complex with self-antigen derived from dopamine monooxygenase.
Components
  • Beta-2-microglobulin
  • Dopamine beta-hydroxylase
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • T cell receptor alpha variable 14-1,T-cell receptor alpha chain C region
  • T-cell receptor beta chain V region C5,T-cell receptor beta-1 chain C region
KeywordsIMMUNE SYSTEM / LCMV / cross-reactivity / MHC class I / TCR / APL
Function / homology
Function and homology information


Catecholamine biosynthesis / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / regulation of vascular endothelial cell proliferation / homoiothermy / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / Phosphorylation of CD3 and TCR zeta chains ...Catecholamine biosynthesis / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / regulation of vascular endothelial cell proliferation / homoiothermy / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / norepinephrine biosynthetic process / Generation of second messenger molecules / chromaffin granule membrane / Downstream TCR signaling / behavioral response to ethanol / dopamine catabolic process / fear response / maternal behavior / alpha-beta T cell receptor complex / vasoconstriction / L-ascorbic acid binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / leukocyte migration / T cell receptor complex / response to pain / transport vesicle membrane / associative learning / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / blood vessel remodeling / cellular defense response / positive regulation of vasoconstriction / Neutrophil degranulation / response to amphetamine / secretory granule membrane / lumenal side of endoplasmic reticulum membrane / locomotory behavior / 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 / 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 / visual learning / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / memory / centriolar satellite / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / glucose homeostasis / negative regulation of neuron projection development / iron ion transport / positive regulation of cold-induced thermogenesis / T cell differentiation in thymus / protein refolding / secretory granule lumen / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / copper ion binding / external side of plasma membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / Copper-dependent monooxygenases, DOMON domain / DOMON domain / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal ...Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / Copper-dependent monooxygenases, DOMON domain / DOMON domain / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / : / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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
T cell receptor alpha variable 14-1 / T-cell receptor alpha chain constant / T-cell receptor beta-1 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / T-cell receptor beta chain V region C5 / Dopamine beta-hydroxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsAchour, A. / Sandalova, T. / Allerbring, E.
CitationJournal: to be published
Title: Structural basis for CD8+ T cells auto-reactivity in LCMV infection
Authors: Allerbring, E. / Duru, A.D. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
G: T cell receptor alpha variable 14-1,T-cell receptor alpha chain C region
H: T-cell receptor beta chain V region C5,T-cell receptor beta-1 chain C region
P: Dopamine beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7076
Polymers96,6155
Non-polymers921
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint-42 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.383, 46.622, 90.059
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABGH

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 13794.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein T cell receptor alpha variable 14-1,T-cell receptor alpha chain C region


Mass: 23030.656 Da / Num. of mol.: 1 / Fragment: UNP residues 22-120,UNP residues 1-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav14-1, Tcra / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JF94, UniProt: P01849
#4: Protein T-cell receptor beta chain V region C5,T-cell receptor beta-1 chain C region


Mass: 26663.633 Da / Num. of mol.: 1 / Fragment: UNP residues 11-122,UNP residues 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213, UniProt: P01852

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide Dopamine beta-hydroxylase / Dopamine beta-monooxygenase


Mass: 1038.173 Da / Num. of mol.: 1 / Fragment: UNP residues 557-565 / Mutation: L3P / Source method: obtained synthetically / Details: Pro3 is replacement of Leu3 of wild type / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q64237, dopamine beta-monooxygenase

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Non-polymers , 2 types, 176 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris HCl pH 8.0 PEG 6000 / PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.89→50.5 Å / Num. obs: 80434 / % possible obs: 93.9 % / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8616 / % possible all: 69.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S7U.pdb

1s7u


Resolution: 1.89→50.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.686 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24752 4052 5 %RANDOM
Rwork0.18726 ---
obs0.19028 76382 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.842 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å20.35 Å2
2--2.71 Å20 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 1.89→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6494 0 6 175 6675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196688
X-RAY DIFFRACTIONr_bond_other_d0.0010.026074
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.9389087
X-RAY DIFFRACTIONr_angle_other_deg0.7043.00214003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49224.043329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.354151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1561539
X-RAY DIFFRACTIONr_chiral_restr0.0720.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217615
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021610
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.283312760
X-RAY DIFFRACTIONr_sphericity_free30.275568
X-RAY DIFFRACTIONr_sphericity_bonded15.756512676
LS refinement shellResolution: 1.889→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 206 -
Rwork0.261 3746 -
obs--62.4 %

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