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- PDB-2pyf: Crystal Structures of High Affinity Human T-Cell Receptors Bound ... -

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Basic information

Entry
Database: PDB / ID: 2pyf
TitleCrystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry Unbound TCR Clone 5-1
Components(T-Cell Receptor, ...) x 2
KeywordsIMMUNE SYSTEM / T-CELL RECEPTOR / CDR3 / PHAGE DISPLAY / MUTANT / HIGH AFFINITY / NY-ESO-1
Function / homology
Function and homology information


alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway ...alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / response to bacterium / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / T cell receptor alpha chain constant / : / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. ...Sami, M. / Rizkallah, P.J. / Dunn, S. / Li, Y. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Molloy, P. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
CitationJournal: Protein Eng.Des.Sel. / Year: 2007
Title: Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry
Authors: Sami, M. / Rizkallah, P.J. / Dunn, S. / Molloy, P. / Moysey, R. / Vuidepot, A. / Baston, E. / Todorov, P. / Yi, L. / Gao, F. / Boulter, J.M. / Jakobsen, B.K.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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
Remark 999Sequence No suitable database reference was found for Chains A and B at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-Cell Receptor, Alpha Chain
B: T-Cell Receptor, Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,82913
Polymers49,4582
Non-polymers1,37111
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-84 kcal/mol
Surface area20580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)42.964, 59.805, 81.799
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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T-Cell Receptor, ... , 2 types, 2 molecules AB

#1: Protein T-Cell Receptor, Alpha Chain


Mass: 22437.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6PIZ8, UniProt: P01848*PLUS
#2: Protein T-Cell Receptor, Beta Chain


Mass: 27020.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6NS87

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Non-polymers , 4 types, 171 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 85 mM Na HEPES buffer pH7.5, 8.5 % iso-propanol, 17% PEG 4000, 15% glycerol, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2005 / Details: MIRROR + MONOCHROMATOR
RadiationMonochromator: SI (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 20741 / % possible obs: 97 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 3.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.3 / Num. measured all: 2196 / Num. unique all: 701 / Rsym value: 0.079 / % possible all: 90.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BNR

2bnr


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.783 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.426 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29484 1064 5.2 %RANDOM
Rwork0.20919 ---
obs0.21348 19532 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.403 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å21.45 Å2
2---0.46 Å20 Å2
3---1.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 83 160 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223648
X-RAY DIFFRACTIONr_bond_other_d0.0030.022457
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9634953
X-RAY DIFFRACTIONr_angle_other_deg0.7223.0035977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2695446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.47824.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.7721519
X-RAY DIFFRACTIONr_chiral_restr0.0920.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02719
X-RAY DIFFRACTIONr_nbd_refined0.2040.3768
X-RAY DIFFRACTIONr_nbd_other0.2150.32694
X-RAY DIFFRACTIONr_nbtor_refined0.1820.51680
X-RAY DIFFRACTIONr_nbtor_other0.0930.51767
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5262
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0750.55
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.333
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.513
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.77122335
X-RAY DIFFRACTIONr_mcbond_other0.6682892
X-RAY DIFFRACTIONr_mcangle_it4.10233619
X-RAY DIFFRACTIONr_scbond_it5.79541548
X-RAY DIFFRACTIONr_scangle_it7.77261334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 74 -
Rwork0.293 1332 -
obs--89.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.48640.446-0.98843.5649-1.05333.02130.01390.6428-0.0277-0.10650.19340.3598-0.193-0.4267-0.2073-0.16290.0051-0.03090.07550.0178-0.1277-15.80731.69757.453
22.58950.7303-0.48515.1626-0.2113.65320.1205-0.3988-0.02290.1008-0.079-0.0479-0.19160.0242-0.0415-0.1284-0.01630.0357-0.0979-0.0072-0.08540.8308-15.318833.5713
32.2285-0.28781.40512.511-0.00935.4619-0.0580.1259-0.0227-0.01450.25790.0994-0.6028-0.0055-0.1999-0.05880.0140.0417-0.09610.0432-0.07190.829616.43539.7467
42.1004-0.1024-1.12751.9398-0.39991.75480.0337-0.08170.05360.10630.0074-0.12-0.10670.129-0.0411-0.11890.0054-0.0431-0.0577-0.0059-0.092512.4177-7.795826.0383
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1121 - 112
2X-RAY DIFFRACTION2AA120 - 200120 - 200
3X-RAY DIFFRACTION3BB1 - 1131 - 113
4X-RAY DIFFRACTION4BB120 - 241120 - 241

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