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- PDB-4mnq: TCR-peptide specificity overrides affinity enhancing TCR-MHC inte... -

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Basic information

Entry
Database: PDB / ID: 4mnq
TitleTCR-peptide specificity overrides affinity enhancing TCR-MHC interactions
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Telomerase reverse transcriptase
  • Uncharacterized protein, T-cell receptor, sp3.4 alpha chain
  • V_segment translation product, T-cell receptor beta-1 chain C region
KeywordsIMMUNE SYSTEM / Surface plasmon resonance (SPR) / BIAcoreTM / peptide-major histocompatibility complex (pMHC): T-cell receptor (TCR) / T-cells / high affinity TCR / two-step binding / adoptive therapy / Immunoglobulin / Adaptive immune response
Function / homology
Function and homology information


positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process ...positive regulation of hair cycle / template-free RNA nucleotidyltransferase / positive regulation of transdifferentiation / TERT-RMRP complex / DNA strand elongation / RNA-directed RNA polymerase complex / siRNA transcription / positive regulation of protein localization to nucleolus / telomerase catalytic core complex / RNA-templated DNA biosynthetic process / : / establishment of protein localization to telomere / telomerase activity / nuclear telomere cap complex / alpha-beta T cell receptor complex / siRNA processing / telomerase holoenzyme complex / positive regulation of vascular associated smooth muscle cell migration / telomerase RNA binding / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / DNA biosynthetic process / RNA-templated transcription / CD8 receptor binding / telomeric DNA binding / positive regulation of stem cell proliferation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / mitochondrial nucleoid / antigen processing and presentation of exogenous peptide antigen via MHC class I / negative regulation of cellular senescence / endoplasmic reticulum exit site / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / Telomere Extension By Telomerase / Generation of second messenger molecules / TAP binding / telomere maintenance via telomerase / protection from natural killer cell mediated cytotoxicity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / replicative senescence / positive regulation of Wnt signaling pathway / PD-1 signaling / positive regulation of G1/S transition of mitotic cell cycle / beta-2-microglobulin binding / negative regulation of endothelial cell apoptotic process / T cell receptor binding / response to cadmium ion / detection of bacterium / immunoglobulin complex, circulating / positive regulation of vascular associated smooth muscle cell proliferation / immunoglobulin receptor binding / telomere maintenance / mitochondrion organization / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / positive regulation of nitric-oxide synthase activity / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / complement activation, classical pathway / 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 / positive regulation of glucose import / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen binding / Formation of the beta-catenin:TCF transactivating complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of protein stability / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / PML body / MHC class I protein complex / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / positive regulation of miRNA transcription / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis
Similarity search - Function
: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...: / Telomerase reverse transcriptase, C-terminal extension / Telomerase ribonucleoprotein complex - RNA binding domain / Telomerase reverse transcriptase / Telomerase ribonucleoprotein complex - RNA-binding domain / Telomerase ribonucleoprotein complex - RNA binding domain / 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 / 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 / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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 / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta variable 6-5 / Ig-like domain-containing protein / T-cell receptor, sp3.4 alpha chain / Telomerase reverse transcriptase / 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)
Pan troglodytes (chimpanzee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.742 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Jakobsen, B.K.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: T-cell receptor (TCR)-peptide specificity overrides affinity-enhancing TCR-major histocompatibility complex interactions.
Authors: Cole, D.K. / Miles, K.M. / Madura, F. / Holland, C.J. / Schauenburg, A.J. / Godkin, A.J. / Bulek, A.M. / Fuller, A. / Akpovwa, H.J. / Pymm, P.G. / Liddy, N. / Sami, M. / Li, Y. / Rizkallah, ...Authors: Cole, D.K. / Miles, K.M. / Madura, F. / Holland, C.J. / Schauenburg, A.J. / Godkin, A.J. / Bulek, A.M. / Fuller, A. / Akpovwa, H.J. / Pymm, P.G. / Liddy, N. / Sami, M. / Li, Y. / Rizkallah, P.J. / Jakobsen, B.K. / Sewell, A.K.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Telomerase reverse transcriptase
D: Uncharacterized protein, T-cell receptor, sp3.4 alpha chain
E: V_segment translation product, T-cell receptor beta-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5708
Polymers94,3545
Non-polymers2163
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-56 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.220, 48.490, 118.070
Angle α, β, γ (deg.)90.000, 107.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 4 molecules ABDE

#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): Rosetta DE3 / References: UniProt: P61769
#4: Protein Uncharacterized protein, T-cell receptor, sp3.4 alpha chain


Mass: 22245.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pan troglodytes (chimpanzee), (gene. exp.) Homo sapiens (human)
Gene: LOC452776 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: H2RG00, UniProt: K7N5M9
#5: Protein V_segment translation product, T-cell receptor beta-1 chain C region


Mass: 27135.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCRBV13S1, TRBC1 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: A0A585, UniProt: P01850

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Telomerase reverse transcriptase / HEST2 / Telomerase catalytic subunit / Telomerase-associated protein 2 / TP2


Mass: 1142.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: MAGE hTERT 540-548 sequence / Source: (synth.) Homo sapiens (human) / References: UniProt: O14746, RNA-directed DNA polymerase

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Non-polymers , 3 types, 24 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: TRIS 0.02M, 20% PEG 4000, 0.01M NaCl, 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
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 30, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.74→42.15 Å / Num. obs: 26577 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.74-2.811.60.9091.8185.6
12.26-42.151.40.03919166.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.16data scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.742→42.15 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 1 / SU B: 37.958 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28438 1344 5.1 %RANDOM
Rwork0.214 ---
obs0.21767 25218 97.65 %-
all-26562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.78 Å2
2--0.7 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.742→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6649 0 14 21 6684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196851
X-RAY DIFFRACTIONr_bond_other_d0.0010.026168
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9279317
X-RAY DIFFRACTIONr_angle_other_deg0.8283.00214172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4455820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21923.864352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.491151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2381546
X-RAY DIFFRACTIONr_chiral_restr0.0890.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4662.9813295
X-RAY DIFFRACTIONr_mcbond_other1.4662.9813294
X-RAY DIFFRACTIONr_mcangle_it2.4274.4684110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6453.1083556
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.742→2.813 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 95 -
Rwork0.343 1858 -
obs--98.74 %
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)
15.02691.33110.46262.58040.45433.48730.12430.3027-0.0235-0.0875-0.00930.177-0.0274-0.4157-0.1150.0320.0253-0.00680.0829-0.00050.086432.67940.2716-12.4552
22.3432-1.4284-1.50228.82645.70468.87370.0369-0.06910.72080.1561-0.3570.3512-0.7887-0.71680.32010.32240.0779-0.01020.3287-0.03460.492916.44114.780115.6706
35.69391.6877-2.81453.6395-3.37459.48250.0107-0.4098-0.11330.4250.0890.0084-0.09040.0885-0.09980.0680.0325-0.0070.0612-0.03720.133933.5477-0.178614.9051
43.3409-0.46630.84412.4697-2.127111.8846-0.09560.49120.1172-0.39490.07820.0084-0.2823-1.08180.01740.16740.0394-0.04840.44380.00250.313726.0301-2.6319-43.1843
57.9537-1.4320.04985.9832-0.24697.22870.25270.4527-0.4434-0.4365-0.0550.1590.1114-0.8568-0.19780.2298-0.1257-0.03360.74680.0320.225931.7237-13.6212-73.9581
64.1345-0.4797-0.60085.26783.740310.6931-0.13560.0836-0.4321-0.11650.2848-0.28730.70330.4341-0.14920.14130.0336-0.02760.16440.01030.239944.9337-14.9881-36.8261
73.6326-0.24060.73253.8319-0.87537.9096-0.04230.3542-0.26450.02090.1302-0.22370.2130.0557-0.08780.1792-0.0990.10470.4551-0.22110.273646.4708-13.0984-66.8903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D1 - 115
6X-RAY DIFFRACTION5D116 - 210
7X-RAY DIFFRACTION6E0 - 115
8X-RAY DIFFRACTION7E116 - 250

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