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- PDB-4jfd: Preservation of peptide specificity during TCR-MHC contact domina... -

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Basic information

Entry
Database: PDB / ID: 4jfd
TitlePreservation of peptide specificity during TCR-MHC contact dominated affinity enhancement of a melanoma-specific TCR
Components
  • (High Affinity TCR ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Melanoma peptide
KeywordsIMMUNE SYSTEM / HLA / TCR / Melanoma / High Affinity / Immunoglobulin
Function / homology
Function and homology information


alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / Translocation of ZAP-70 to Immunological synapse ...alpha-beta T cell receptor complex / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane
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 / Beta-2-Microglobulin ...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 / 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
T cell receptor alpha chain constant / T cell receptor beta constant 1 / 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: 2.46 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Madura, F. / Sewell, A.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: T-cell receptor specificity maintained by altered thermodynamics.
Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / ...Authors: Madura, F. / Rizkallah, P.J. / Miles, K.M. / Holland, C.J. / Bulek, A.M. / Fuller, A. / Schauenburg, A.J. / Miles, J.J. / Liddy, N. / Sami, M. / Li, Y. / Hossain, M. / Baker, B.M. / Jakobsen, B.K. / Sewell, A.K. / Cole, D.K.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2013Group: Database references
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Melanoma peptide
D: High Affinity TCR Alpha Chain
E: High Affinity TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31217
Polymers94,0925
Non-polymers1,22012
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13380 Å2
ΔGint-207 kcal/mol
Surface area38920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.490, 121.490, 82.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Melanoma peptide


Mass: 999.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Heteroclitic G4A version of Melanoma epitope

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High Affinity TCR ... , 2 types, 2 molecules DE

#4: Protein High Affinity TCR Alpha Chain


Mass: 21739.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01848*PLUS
#5: Protein High Affinity TCR Beta Chain


Mass: 27522.686 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseatta DE3 / References: UniProt: P01850*PLUS

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Non-polymers , 3 types, 137 molecules

#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.25 Å3/Da / Density % sol: 62.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M TRIS, 15% PEG 4000, 17.4% glycerol, pH 7.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorDetector: CCD / Date: Oct 8, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.46→54.332 Å / Num. all: 44185 / Num. obs: 44185 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.46-2.528.40.7512748932720.75100
2.52-2.598.40.6131.32648831540.613100
2.59-2.678.40.51.52580430710.5100
2.67-2.758.30.39422491429840.394100
2.75-2.848.40.3142.52457229220.314100
2.84-2.948.40.2343.32335727870.234100
2.94-3.058.40.1774.42276327150.177100
3.05-3.178.40.1335.82194426210.133100
3.17-3.318.40.17.72100425140.1100
3.31-3.488.20.08391986224080.083100
3.48-3.668.20.07110.31863622720.071100
3.66-3.8980.05612.71725321680.056100
3.89-4.157.90.04814.21568819980.048100
4.15-4.4980.043151538019120.043100
4.49-4.918.10.04115.11437917670.041100
4.91-5.497.90.04115.31237215670.041100
5.49-6.348.20.041161164814160.041100
6.34-7.778.20.03816.9968211830.038100
7.77-10.997.90.03120.773459300.03199.9
10.99-54.3326.90.03318.236295240.03397.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 48.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å54.33 Å
Translation2.5 Å54.33 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→54.33 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2458 / WRfactor Rwork: 0.2018 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8561 / SU B: 14.365 / SU ML: 0.164 / SU R Cruickshank DPI: 0.3447 / SU Rfree: 0.2503 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 2225 5 %RANDOM
Rwork0.2021 ---
obs0.2045 44161 100 %-
all-44161 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 229.81 Å2 / Biso mean: 68.3754 Å2 / Biso min: 17.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.46→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 66 125 6820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216869
X-RAY DIFFRACTIONr_bond_other_d0.0020.024633
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.949342
X-RAY DIFFRACTIONr_angle_other_deg0.701311210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6645822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.55523.919347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.085151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6761547
X-RAY DIFFRACTIONr_chiral_restr0.1730.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021450
X-RAY DIFFRACTIONr_mcbond_it2.89724127
X-RAY DIFFRACTIONr_mcbond_other0.89721659
X-RAY DIFFRACTIONr_mcangle_it4.75236656
X-RAY DIFFRACTIONr_scbond_it7.37342742
X-RAY DIFFRACTIONr_scangle_it9.6962686
LS refinement shellResolution: 2.46→2.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 167 -
Rwork0.365 3095 -
all-3262 -
obs--100 %
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)
13.55830.377-0.90843.7896-0.87623.5793-0.0420.028-0.2902-0.0979-0.0327-0.19310.27170.3310.07470.04530.02780.04840.2349-0.00770.109455.1354-7.621126.6884
210.9707-3.30981.89773.44632.86995.4008-0.5046-0.1202-0.72930.29021.1187-0.48130.47631.744-0.61411.27530.25310.44851.36870.31531.459479.1729-33.508821.7373
34.47450.3932-1.81896.9570.69477.4867-0.4460.1955-1.1484-0.3974-0.12140.0071.9273-0.18810.56740.56570.02950.16780.3024-0.00590.429364.896-23.30436.7397
44.4887-1.0793-0.97442.26760.54462.8998-0.1-0.51150.07560.23760.06440.02160.08390.1950.03560.043-0.0323-0.0070.19430.03670.082334.66392.512548.1479
513.7955-0.81594.39587.62760.114912.5607-0.2654-1.21930.1050.63030.12140.1207-0.0129-0.72260.1440.5290.07790.03260.6119-0.00630.34526.938818.94957.8143
69.1678-2.7369-0.48071.2774-0.17111.49080.26610.4870.0937-0.3622-0.19520.017-0.16890.0912-0.07090.27750.0195-0.01280.14480.06070.052229.47996.07125.4731
74.5194-0.33741.59333.43342.961410.8043-0.2245-0.63770.47990.37610.1898-0.2634-0.68790.39530.03470.27440.0138-0.09260.18110.00420.24299.778623.559142.2236
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 - 115
6X-RAY DIFFRACTION5D116 - 196
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 244

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