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- PDB-2oi9: Structure of the 2C/Ld/QL9 allogeneic complex -

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Basic information

Entry
Database: PDB / ID: 2oi9
TitleStructure of the 2C/Ld/QL9 allogeneic complex
Components
  • Major Histocompatibility Complex protein
  • T cell receptor alpha chain
  • T cell receptor beta chain
  • peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)
KeywordsIMMUNE SYSTEM / TCR / MHC
Function / homology
Function and homology information


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 tolerance induction / natural killer cell lectin-like receptor binding / T cell receptor complex ...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 tolerance induction / natural killer cell lectin-like receptor binding / T cell receptor complex / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / 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 interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / 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 / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
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 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...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 / 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
Beta-chain / T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGarcia, K.C. / Colf, L.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: How a single T cell receptor recognizes both self and foreign MHC.
Authors: Colf, L.A. / Bankovich, A.J. / Hanick, N.A. / Bowerman, N.A. / Jones, L.L. / Kranz, D.M. / Garcia, K.C.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major Histocompatibility Complex protein
B: T cell receptor alpha chain
C: T cell receptor beta chain
Q: peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Theoretical massNumber of molelcules
Total (without water)47,7614
Polymers47,7614
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-30 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.171, 163.171, 95.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

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Components

#1: Protein Major Histocompatibility Complex protein /


Mass: 20941.064 Da / Num. of mol.: 1 / Fragment: alpha 1,2 domains / Mutation: F9Y, V12T, I23T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01897
#2: Protein T cell receptor alpha chain / V alpha


Mass: 12487.985 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01738
#3: Protein T cell receptor beta chain / V beta


Mass: 13268.437 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A2NTY6
#4: Protein/peptide peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Mass: 1063.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized peptide
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.9M sodium dihydrogen phosphate, 0.01M di-potassium hydrogen phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.35→141.42 Å / Num. obs: 29820 / % possible obs: 99.92 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 17.3
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.5 / % possible all: 99.96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LDP, 2CKB

1ldp

2ckb


Resolution: 2.35→60 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.221 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: FUSION PROTEIN COMPRISES chain B (T cell receptor alpha chain), the LINKER (GGGGSGGGGSGGGGSGGGGS), chain C(T cell receptor beta chain) and c-terminal tail with sequence HHHHHH. There is not ...Details: FUSION PROTEIN COMPRISES chain B (T cell receptor alpha chain), the LINKER (GGGGSGGGGSGGGGSGGGGS), chain C(T cell receptor beta chain) and c-terminal tail with sequence HHHHHH. There is not LINK record for chain B and LINKER, nor LINK for LINKER and chain C because the LINKER was not visible. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22629 1580 5 %RANDOM
Rwork0.22046 ---
obs0.22076 29820 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 0 176 3401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213320
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9374499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3365400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.623.118170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87515509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6491527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022614
X-RAY DIFFRACTIONr_nbd_refined0.2420.21487
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22232
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.210
X-RAY DIFFRACTIONr_mcbond_it1.1281.52046
X-RAY DIFFRACTIONr_mcangle_it1.56323200
X-RAY DIFFRACTIONr_scbond_it2.27131482
X-RAY DIFFRACTIONr_scangle_it3.4034.51299
LS refinement shellResolution: 2.353→2.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 108 -
Rwork0.313 2165 -
obs--99.96 %

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