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- PDB-1g6r: A FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST T... -

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Basic information

Entry
Database: PDB / ID: 1g6r
TitleA FUNCTIONAL HOT SPOT FOR ANTIGEN RECOGNITION IN A SUPERAGONIST TCR/MHC COMPLEX
Components
  • ALPHA T CELL RECEPTOR
  • BETA T CELL RECEPTOR
  • BETA-2 MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
  • SIYR PEPTIDE
KeywordsIMMUNE SYSTEM / T CELL ANTIGEN RECEPTOR / MAJOR HISTOCOMPATIBILITY COMPLEX / SUPERAGONIST
Function / homology
Function and homology information


MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway ...MHC class Ib protein complex / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / ER-Phagosome pathway / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / regulation of membrane depolarization / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / inner ear development / CD8 receptor binding / beta-2-microglobulin binding / endoplasmic reticulum exit site / MHC class I protein binding / TAP binding / cellular defense response / 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 / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / iron ion transport / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / antimicrobial humoral immune response mediated by antimicrobial peptide / late endosome membrane / negative regulation of neuron projection development / antibacterial humoral response / protein-folding chaperone binding / protein refolding / cellular response to lipopolysaccharide / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / learning or memory / early endosome / defense response to bacterium / defense response to Gram-positive bacterium / immune response / receptor ligand activity / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / : / 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, 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/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
T-cell receptor alpha chain V region PHDS58 / T-cell receptor beta-1 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDegano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
Citation
Journal: Immunity / Year: 2000
Title: A functional hot spot for antigen recognition in a superagonist TCR/MHC complex.
Authors: Degano, M. / Garcia, K.C. / Apostolopoulos, V. / Rudolph, M.G. / Teyton, L. / Wilson, I.A.
#1: Journal: Science / Year: 1998
Title: Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen
Authors: Garcia, K.C. / Degano, M. / Pease, L.R. / Huang, M. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
History
DepositionNov 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 13, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA T CELL RECEPTOR
B: BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
L: BETA-2 MICROGLOBULIN
P: SIYR PEPTIDE
C: ALPHA T CELL RECEPTOR
D: BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
M: BETA-2 MICROGLOBULIN
Q: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)185,94210
Polymers185,94210
Non-polymers00
Water00
1
A: ALPHA T CELL RECEPTOR
B: BETA T CELL RECEPTOR
H: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
L: BETA-2 MICROGLOBULIN
P: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)92,9715
Polymers92,9715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ALPHA T CELL RECEPTOR
D: BETA T CELL RECEPTOR
I: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE
M: BETA-2 MICROGLOBULIN
Q: SIYR PEPTIDE


Theoretical massNumber of molelcules
Total (without water)92,9715
Polymers92,9715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)297.710, 94.570, 84.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ALPHA T CELL RECEPTOR


Mass: 22298.889 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01738
#2: Protein BETA T CELL RECEPTOR


Mass: 26284.180 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01852
#3: Protein MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULE


Mass: 31648.322 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01901
#4: Protein BETA-2 MICROGLOBULIN


Mass: 11704.359 Da / Num. of mol.: 2 / Fragment: NON-COVALENTLY ASSOCIATED WITH ENTITY 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#5: Protein/peptide SIYR PEPTIDE


Mass: 1035.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.2
Details: 0.2 M Tris/acetate, 10% PEG 6000, pH 7.2, VAPOR DIFFUSION, temperature 22K
Crystal grow
*PLUS
Method: unknown
Details: used macroseeding, Garcia, K.C., (1997) Proc.Natl.Acad.Sci.USA., 94, 13838.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG400011
20.2 MTris acetate11
30.1 M11NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 52209 / % possible obs: 83.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 20.3
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.9 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.3267 1316 RANDOM
Rwork0.2976 --
all-52177 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13100 0 0 0 13100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_improper_angle_d0.86
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 2 % / Rfactor obs: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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