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Basic information

Entry
Database: PDB / ID: 4jff
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 motif
KeywordsIMMUNE SYSTEM / HLA / TCR / Melanoma motif / High Affinity
Function / homology
Function and homology information


melanosome membrane / 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 ...melanosome membrane / 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 / Regulation of MITF-M-dependent genes involved in pigmentation / 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 / trans-Golgi network / 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 / melanosome / 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
Similarity search - Function
Protein melan-A / Protein melan-A / 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 ...Protein melan-A / Protein melan-A / 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 / Melanoma antigen recognized by T-cells 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 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 1.4Apr 2, 2014Group: Source and taxonomy
Revision 1.5Oct 16, 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 motif
D: High Affinity TCR Alpha Chain
E: High Affinity TCR Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,37514
Polymers94,2265
Non-polymers1,1499
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-152 kcal/mol
Surface area38150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.440, 121.440, 82.300
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 motif


Mass: 985.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16655*PLUS

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

#4: Protein High Affinity TCR Alpha Chain


Mass: 21887.055 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, 168 molecules

#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M TRIS, 15% PEG 4000, 17.4% Glycerol, pH 7.0, 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: 2.43→68.13 Å / Num. all: 45232 / Num. obs: 45232 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 55.88 Å2 / Rsym value: 0.091 / Net I/σ(I): 14.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.43-2.498.40.9090.82796633330.909100
2.49-2.568.40.71812715332390.718100
2.56-2.648.40.6141.22641431500.614100
2.64-2.728.40.4891.52574330740.489100
2.72-2.818.40.3971.82480329610.397100
2.81-2.918.40.312.32391128560.31100
2.91-3.028.30.2313.12326627870.231100
3.02-3.148.30.1724.32239226840.172100
3.14-3.288.30.1315.62131225670.131100
3.28-3.448.30.0997.42023124450.099100
3.44-3.628.20.0888.31914723280.088100
3.62-3.848.10.07101804222160.07100
3.84-4.118.10.05911.61693920920.059100
4.11-4.448.10.05112.51577819370.051100
4.44-4.868.10.0512.91467618030.05100
4.86-5.447.90.04913.11284916170.049100
5.44-6.288.20.04913.61163814260.049100
6.28-7.698.10.04614.31000312320.046100
7.69-10.877.90.03617.674659490.036100
10.87-68.12970.03717.337375360.03798.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.06 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å68.13 Å
Translation2.5 Å68.13 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: 2.43→68.129 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2614 / WRfactor Rwork: 0.2108 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8412 / SU B: 14.474 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3472 / SU Rfree: 0.2601 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 2278 5 %RANDOM
Rwork0.2104 ---
obs0.213 45209 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 184.06 Å2 / Biso mean: 54.7259 Å2 / Biso min: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.43→68.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 65 159 6864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0216897
X-RAY DIFFRACTIONr_bond_other_d0.0020.024670
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.949380
X-RAY DIFFRACTIONr_angle_other_deg0.743311302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8335825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.79723.897349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.058151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6161547
X-RAY DIFFRACTIONr_chiral_restr0.1020.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021460
X-RAY DIFFRACTIONr_mcbond_it1.31724134
X-RAY DIFFRACTIONr_mcbond_other0.32521664
X-RAY DIFFRACTIONr_mcangle_it2.46236669
X-RAY DIFFRACTIONr_scbond_it3.71342763
X-RAY DIFFRACTIONr_scangle_it5.47162711
LS refinement shellResolution: 2.43→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 171 -
Rwork0.299 3159 -
all-3330 -
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)
12.98470.2926-0.82692.7466-0.56052.6054-0.02410.0343-0.1549-0.0217-0.042-0.09240.1980.2720.06610.03540.02210.03880.1231-0.01570.079855.0205-7.62526.2875
211.7496-2.9012-1.14894.36721.29993.9334-0.1980.0439-0.5090.1146-0.0596-0.90490.5521.47280.25760.59220.20750.10250.68330.25820.885378.2825-34.957919.6676
33.950.9503-1.28914.81820.51925.5521-0.3520.3723-0.9918-0.5298-0.1453-0.04481.1244-0.09830.49730.33960.05290.14350.2317-0.06420.352664.2059-23.32466.1903
43.3624-1.4161-1.31911.7880.47152.7195-0.096-0.38670.11490.2460.0569-0.0602-0.02650.13510.03910.0467-0.0273-0.0110.11250.00490.065234.79392.778947.9118
511.72152.67533.62356.85572.08949.4766-0.3003-0.71720.10560.0230.19760.3235-0.0296-0.78970.10270.32380.08040.03410.46980.05410.18977.007719.100657.8801
68.5197-2.1693-0.16510.8788-0.08742.05470.26490.47710.044-0.3188-0.19150.007-0.17570.0227-0.07340.23640.0625-0.00590.07130.0330.040129.45146.275625.3532
73.08650.0091.9742.89423.208210.1868-0.1004-0.36980.24630.12810.1163-0.103-0.5220.1493-0.01580.11570.014-0.02620.11270.01950.16769.561623.697642.2833
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 - 197
7X-RAY DIFFRACTION6E1 - 115
8X-RAY DIFFRACTION7E116 - 244

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