[English] 日本語
Yorodumi
- PDB-6g9q: Ternary complex of P14 TCR with murine MHC class I H-2 Db in comp... -

+
Open data


ID or keywords:

Loading...

-
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-microglobulinBeta-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


regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / homoiothermy / regulation of vascular endothelial cell proliferation / chromaffin granule lumen ...regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / homoiothermy / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / norepinephrine biosynthetic process / PD-1 signaling / Generation of second messenger molecules / varicosity / chromaffin granule membrane / Downstream TCR signaling / behavioral response to ethanol / maternal behavior / dopamine catabolic process / alpha-beta T cell receptor complex / fear response / vasoconstriction / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / L-ascorbic acid binding / 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 / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / T cell receptor complex / response to pain / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transport vesicle membrane / positive regulation of interleukin-13 production / leukocyte migration / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / associative learning / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / centriolar satellite / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / blood vessel remodeling / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / positive regulation of vasoconstriction / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / response to amphetamine / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / secretory granule membrane / 14-3-3 protein binding / locomotory behavior / lumenal side of endoplasmic reticulum membrane / response to bacterium / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / visual learning / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / terminal bouton
Similarity search - Function
Copper-dependent monooxygenases, DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / 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-dependent monooxygenases, DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / 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 / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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 / 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

-
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

-
Non-polymers , 2 types, 176 molecules

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


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


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more