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- PDB-2e7l: Structure of a high-affinity mutant of the 2C TCR in complex with... -

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Basic information

Entry
Database: PDB / ID: 2e7l
TitleStructure of a high-affinity mutant of the 2C TCR in complex with Ld/QL9
Components
  • Beta-chain
  • Cytotoxic Tcell receptor
  • H-2 class I histocompatibility antigen, L-D alpha chain
  • Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)
KeywordsIMMUNE SYSTEM / TCR / MHC
Function / homology
Function and homology information


T cell receptor complex / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / adaptive immune response ...T cell receptor complex / 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 / lumenal side of endoplasmic reticulum membrane / MHC class I protein complex / defense response / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane / signaling receptor binding / extracellular space
Similarity search - Function
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 / MHC class I-like antigen recognition-like ...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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytotoxic Tcell receptor / Beta-chain / 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: 2.5 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 11, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references
Revision 1.4Oct 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 / 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: Cytotoxic Tcell receptor
B: Cytotoxic Tcell receptor
C: Beta-chain
D: Beta-chain
E: H-2 class I histocompatibility antigen, L-D alpha chain
F: H-2 class I histocompatibility antigen, L-D alpha chain
P: Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)
Q: Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Theoretical massNumber of molelcules
Total (without water)96,4718
Polymers96,4718
Non-polymers00
Water3,117173
1
A: Cytotoxic Tcell receptor
D: Beta-chain
E: H-2 class I histocompatibility antigen, L-D alpha chain
Q: Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Theoretical massNumber of molelcules
Total (without water)48,2354
Polymers48,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-26 kcal/mol
Surface area17740 Å2
MethodPISA
2
B: Cytotoxic Tcell receptor
C: Beta-chain
F: H-2 class I histocompatibility antigen, L-D alpha chain
P: Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Theoretical massNumber of molelcules
Total (without water)48,2354
Polymers48,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.540, 113.540, 177.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11F-182-

HOH

DetailsBiological unit is defined by chains D, A, Q, E. NCS of biological unit defined by chains B, C, P, F.

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Components

#1: Protein Cytotoxic Tcell receptor / V alpha / T cell receptor alpha chain


Mass: 12698.222 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-132
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: A2NTU7
#2: Protein Beta-chain / V beta / T cell receptor beta chain


Mass: 13268.437 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-144
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
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain / Major Histocompatibility Complex protein


Mass: 21205.498 Da / Num. of mol.: 2 / Fragment: alpha 1,2 domains (UNP RESIDUES 25-205)
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
#4: Protein/peptide Peptide (GLN)(LEU)(SER)(PRO)(PHE)(PRO)(PHE)(ASP)(LEU)


Mass: 1063.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic Peptide
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERS 94-98 IN CHAINS A, B AND RESIDUE NUMBERS 64, 99-104 IN CHAINS C, D ARE SIMPLY ...RESIDUE NUMBERS 94-98 IN CHAINS A, B AND RESIDUE NUMBERS 64, 99-104 IN CHAINS C, D ARE SIMPLY SKIPPED. CHAINS A AND D, CHAINS B AND C WERE EXPRESSED AS A SINGLE-CHAIN CONSTRUCT, AND WERE DIVIDED IN THE CRYSTAL STRUCTURE TO MATCH PREVIOUS CRYSTAL STRUCTURES AND BECAUSE THE LINKER WAS NOT VISIBLE. ONE FUSION PROTEIN COMPRISES CHAIN A, THE LINKER, CHAIN D AND C-TERMINAL TAIL, ANOTHER FUSION PROTEIN COMPRISES CHAIN B, THE LINKER, CHAIN C AND C-TERMINAL TAIL. THE LINKER IS NGGGGSGGGGSGGGGSGGGGS AND C-TERMINAL TAIL SSALEHHHHHH. FOR CHAIN E, F, THE SEQUENCE DATABASE REFERENCE DOES NOT CURRENTLY EXIST.

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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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium phosphate, 20% PEG 3350, 0.1M Tris, pH 8.5, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 9, 2006
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→95.78 Å / Num. obs: 39001 / % possible obs: 99.87 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 29
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 12 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 4.4 / % possible all: 99.06

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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: 2OI9

2oi9


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.686 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.421 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24562 2064 5 %RANDOM
Rwork0.224 ---
obs0.2251 39001 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.258 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6509 0 0 173 6682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0216700
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.9379089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2065808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85523.035346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.175151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4311556
X-RAY DIFFRACTIONr_chiral_restr0.0820.2920
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025303
X-RAY DIFFRACTIONr_nbd_refined0.2150.22874
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4270.226
X-RAY DIFFRACTIONr_mcbond_it1.1691.54137
X-RAY DIFFRACTIONr_mcangle_it1.39926446
X-RAY DIFFRACTIONr_scbond_it2.16533013
X-RAY DIFFRACTIONr_scangle_it3.2764.52643
LS refinement shellResolution: 2.495→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 135 -
Rwork0.301 2815 -
obs--99.06 %

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