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- PDB-5c07: 1E6 TCR in complex with HLA-A02 carrying YQFGPDFPIA -

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Basic information

Entry
Database: PDB / ID: 5c07
Title1E6 TCR in complex with HLA-A02 carrying YQFGPDFPIA
Components
  • 1E6 TCR Alpha Chain
  • 1E6 TCR Beta Chain
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Marker peptide
KeywordsIMMUNE SYSTEM / IMMUNO / HLA-A02 / 1E6-TCR / Cross-reactivity
Function / homology
Function and homology information


T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation ...T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP 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 / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface
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-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 / 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 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
T cell receptor alpha variable 12-3 / T cell receptor beta variable 12-4 / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å
AuthorsRizkallah, P.J. / Bulek, A.M. / Cole, D.K. / Sewell, A.K.
CitationJournal: J.Clin.Invest. / Year: 2016
Title: Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity.
Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / ...Authors: Cole, D.K. / Bulek, A.M. / Dolton, G. / Schauenberg, A.J. / Szomolay, B. / Rittase, W. / Trimby, A. / Jothikumar, P. / Fuller, A. / Skowera, A. / Rossjohn, J. / Zhu, C. / Miles, J.J. / Peakman, M. / Wooldridge, L. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,92332
Polymers191,14310
Non-polymers1,78022
Water9,908550
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Marker peptide
D: 1E6 TCR Alpha Chain
E: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,04611
Polymers95,5715
Non-polymers4746
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Marker peptide
I: 1E6 TCR Alpha Chain
J: 1E6 TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,87721
Polymers95,5715
Non-polymers1,30516
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.700, 100.470, 122.100
Angle α, β, γ (deg.)96.950, 98.110, 96.610
Int Tables number1
Space group name H-MP1

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / HLA-A02 Heavy Chain


Mass: 32082.512 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein 1E6 TCR Alpha Chain


Mass: 22428.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J271*PLUS
#5: Protein 1E6 TCR Beta Chain


Mass: 28026.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J2E0*PLUS

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide Marker peptide


Mass: 1154.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 572 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M sodium cholride, 0.1M HEPES pH7, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.108→49.413 Å / Num. all: 113252 / Num. obs: 113252 / % possible obs: 97 % / Redundancy: 2.2 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.069 / Rsym value: 0.049 / Net I/av σ(I): 12.257 / Net I/σ(I): 11.7 / Num. measured all: 246727
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.11-2.162.20.3582.21806283040.3490.3582.495.9
2.16-2.222.20.2872.71771280990.2870.2872.996.1
2.22-2.292.20.2453.11736179430.2360.2453.596.3
2.29-2.362.20.2173.61660175800.210.2173.996.4
2.36-2.432.20.1714.51652775430.1730.1714.896.8
2.43-2.522.20.1325.81563671330.140.1325.996.6
2.52-2.622.20.11171524669570.1190.1116.997
2.62-2.722.20.0958.31482167620.0990.0958.296.9
2.72-2.842.20.07510.21405564000.0810.0759.997.3
2.84-2.982.20.05613.31336861420.0630.05612.297.2
2.98-3.142.20.04715.31299459590.050.04714.897.6
3.14-3.332.20.03719.11205555450.0410.03717.997.6
3.33-3.562.20.03121.21136652280.0340.03120.597.8
3.56-3.852.20.0322.11044648450.030.0322.897.8
3.85-4.222.20.02821.7974845140.0290.02824.597.9
4.22-4.712.10.02626.3871640610.0260.02626.398
4.71-5.442.10.02724.1760336250.0280.02726.398.2
5.44-6.672.20.02822.8656130170.0250.02825.998.4
6.67-9.432.20.02822.9512523370.0240.02827.898.2
9.43-49.4132.20.02724.5272412580.0220.02729.596.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.98 Å41.4 Å
Translation6.98 Å41.4 Å

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Processing

Software
NameVersionClassification
SCALA3.3.15data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UTP and 3UTQ

3utp

3utq


Resolution: 2.11→49.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.1917 / FOM work R set: 0.8257 / SU B: 11.18 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2184 / SU Rfree: 0.1864 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.218 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5674 5 %RANDOM
Rwork0.1909 ---
obs0.1932 107577 97.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.13 Å2 / Biso mean: 50.562 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å2-0.18 Å20.12 Å2
2--0.69 Å21 Å2
3----2.55 Å2
Refinement stepCycle: final / Resolution: 2.11→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13450 0 108 550 14108
Biso mean--55.19 44.57 -
Num. residues----1663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01914004
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212611
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.93618988
X-RAY DIFFRACTIONr_angle_other_deg0.957329068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.50151671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79323.649718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.567152259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.32315105
X-RAY DIFFRACTIONr_chiral_restr0.1270.21964
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02115922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023431
X-RAY DIFFRACTIONr_mcbond_it1.6362.0336687
X-RAY DIFFRACTIONr_mcbond_other1.6362.0336686
X-RAY DIFFRACTIONr_mcangle_it2.623.0358357
LS refinement shellResolution: 2.108→2.163 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 429 -
Rwork0.263 7862 -
all-8291 -
obs--95.95 %
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)
12.4773-0.9813-0.40432.6109-0.3523.06990.0085-0.08220.1230.3180.0646-0.0197-0.47630.108-0.07310.1090.0089-0.01790.0585-0.08510.130413.7847-8.064795.4835
22.94160.60121.00462.9231-0.61616.80450.0705-0.54560.06360.5433-0.0397-0.3507-0.03160.3117-0.03080.45190.0094-0.00690.3731-0.09880.23368.4625-14.7958130.6157
33.63541.9643-3.10452.097-1.86534.517-0.0162-0.245-0.26720.03-0.0832-0.06930.30380.00220.09940.16380.0288-0.05860.174-0.03160.15484.7903-27.9709111.9643
41.97051.628-1.33695.4355-3.13173.8683-0.05650.04760.07920.00690.122-0.0702-0.322-0.0571-0.06560.16140.02220.02680.0526-0.09470.232712.724916.307270.5499
51.55740.51272.70435.81471.8285.6132-0.07590.52320.2127-0.5478-0.05860.9665-0.55810.29630.13451.1207-0.11580.06990.81510.18830.67229.600124.137838.2911
63.07090.26732.51411.30840.26166.19740.04520.1108-0.0237-0.13320.03470.0858-0.1401-0.1484-0.07990.0230.00610.00280.0343-0.05030.19597.7616-5.853665.6427
75.07223.4516-1.07025.2424-0.8592.4272-0.20940.45360.3826-0.50630.40590.0479-0.7820.2041-0.19660.6732-0.1360.03290.3849-0.0990.259212.0467.708738.2295
81.41660.9497-0.08972.9313-0.13752.4985-0.17270.0281-0.0835-0.46610.146-0.06650.35880.10850.02670.12260.0027-0.00330.05-0.06740.122812.507263.369449.9259
93.70510.1011-2.02023.17-0.31886.4702-0.07260.31760.0742-0.54160.0407-0.45670.26550.48760.03180.28110.02450.0040.3391-0.05640.235216.800370.435814.6219
102.0744-0.77112.25811.7457-1.28646.1499-0.04080.17160.2375-0.00960.02970.0092-0.193-0.17660.01110.0515-0.00050.02270.1643-0.01070.16194.934281.470230.8867
111.1155-1.04640.63064.5972-3.08344.3503-0.0883-0.0666-0.06040.07510.0477-0.05270.268-0.02250.04060.16420.0238-0.0440.0436-0.08360.20169.305438.463974.2008
126.2072-2.4866-0.90845.41350.69875.1551-0.0976-0.5205-0.49370.32180.16010.73930.6459-0.3601-0.06260.74110.0252-0.00320.50650.14950.4956-0.805829.4469104.1987
135.23320.5313-2.58751.1672-0.32013.72690.1633-0.24590.05080.0598-0.03150.1120.0915-0.2116-0.13190.0399-0.0035-0.05220.0955-0.05830.1392-1.627558.964976.6428
144.8744-2.75461.86973.9282-1.07373.4814-0.1998-0.502-0.27430.2910.2890.13930.4922-0.0277-0.08920.29360.07160.0830.3584-0.02830.2076-2.748745.8715104.5935
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 117
6X-RAY DIFFRACTION5D118 - 200
7X-RAY DIFFRACTION6E1 - 117
8X-RAY DIFFRACTION7E118 - 247
9X-RAY DIFFRACTION8F1 - 180
10X-RAY DIFFRACTION8H1 - 10
11X-RAY DIFFRACTION9F181 - 276
12X-RAY DIFFRACTION10G0 - 99
13X-RAY DIFFRACTION11I1 - 117
14X-RAY DIFFRACTION12I118 - 200
15X-RAY DIFFRACTION13J1 - 117
16X-RAY DIFFRACTION14J118 - 247

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