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- PDB-3rgv: A single TCR bound to MHCI and MHC II reveals switchable TCR conf... -

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Basic information

Entry
Database: PDB / ID: 3rgv
TitleA single TCR bound to MHCI and MHC II reveals switchable TCR conformers
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • Yae62 TCR a chain
  • Yae62 TCR b chain
  • peptide
KeywordsIMMUNE SYSTEM / TCR / MHC / MHC class I
Function / homology
Function and homology information


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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / 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 / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...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
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: 2.9 Å
AuthorsDai, S. / Huseby, E. / Scott-Browne, J. / Rubtsova, K. / Pinilla, C. / Crawford, F. / Marrack, P. / Yin, L. / Kappler, J.W.
CitationJournal: Immunity / Year: 2011
Title: A Single T Cell Receptor Bound to Major Histocompatibility Complex Class I and Class II Glycoproteins Reveals Switchable TCR Conformers.
Authors: Yin, L. / Huseby, E. / Scott-Browne, J. / Rubtsova, K. / Pinilla, C. / Crawford, F. / Marrack, P. / Dai, S. / Kappler, J.W.
History
DepositionApr 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Yae62 TCR a chain
B: Yae62 TCR b chain
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
E: peptide


Theoretical massNumber of molelcules
Total (without water)93,6305
Polymers93,6305
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Yae62 TCR a chain
B: Yae62 TCR b chain


Theoretical massNumber of molelcules
Total (without water)48,6782
Polymers48,6782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-27 kcal/mol
Surface area20320 Å2
MethodPISA
3
C: H-2 class I histocompatibility antigen, K-B alpha chain
D: Beta-2-microglobulin
E: peptide


Theoretical massNumber of molelcules
Total (without water)44,9523
Polymers44,9523
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-24 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.872, 146.409, 168.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody Yae62 TCR a chain


Mass: 22206.318 Da / Num. of mol.: 1 / Mutation: Y84C, C121S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein Yae62 TCR b chain


Mass: 26471.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2K(B)


Mass: 31701.340 Da / Num. of mol.: 1 / Fragment: Residues 22-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K1, H2-K / Plasmid: pAcUW51 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01901
#4: Protein Beta-2-microglobulin


Mass: 11761.411 Da / Num. of mol.: 1 / Fragment: Residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pAcUW51 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01887
#5: Protein/peptide peptide


Mass: 1489.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAcUW51 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm)
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: 3.83 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7 / Details: PEG 3350, pH 7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→19.43 Å / Num. all: 34349 / Num. obs: 30372

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C60 and 2ZSV

3c60

2zsv


Resolution: 2.9→19.43 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7944 / SU ML: 2.4 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1535 5.05 %RANDOM
Rwork0.2019 ---
obs0.2046 30372 92.54 %-
all-34349 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.892 Å2 / ksol: 0.285 e/Å3
Displacement parametersBiso max: 131.24 Å2 / Biso mean: 58.9744 Å2 / Biso min: 24.84 Å2
Baniso -1Baniso -2Baniso -3
1--20.077 Å20 Å20 Å2
2--10.5099 Å2-0 Å2
3---9.5671 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6592 0 0 0 6592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016778
X-RAY DIFFRACTIONf_angle_d1.3489207
X-RAY DIFFRACTIONf_chiral_restr0.09969
X-RAY DIFFRACTIONf_plane_restr0.0051205
X-RAY DIFFRACTIONf_dihedral_angle_d22.1782412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-2.99340.42521090.33722307241682
2.9934-3.09990.40551150.3472164227977
3.0999-3.22350.45181220.35872245236780
3.2235-3.36950.3191380.26962543268191
3.3695-3.54610.24371430.21032675281895
3.5461-3.76680.28921380.19042742288097
3.7668-4.05520.2431410.17782777291898
4.0552-4.45880.20961670.15012758292598
4.4588-5.09390.16891510.13922837298899
5.0939-6.37980.231580.16832833299199
6.3798-19.42960.21371530.177529563109100

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