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- PDB-5m02: Crystal structure of murine P14 TCR / H-2Db with PF, modified gp3... -

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Basic information

Entry
Database: PDB / ID: 5m02
TitleCrystal structure of murine P14 TCR / H-2Db with PF, modified gp33 peptide from LCMV
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND PF
  • Protein Trav14-1,T-cell receptor alpha chain C region
  • T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region
KeywordsIMMUNE SYSTEM / MHC class I / TCR / H-2Db / gp33 / LCMV
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / alpha-beta T cell receptor complex / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
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 ...: / : / 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 / : / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor alpha variable 14-1 / T-cell receptor alpha chain constant / T-cell receptor beta-2 chain C region / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / T-cell receptor beta chain V region C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Lymphocytic choriomeningitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAchour, A. / Sandalova, T. / Sun, R.
CitationJournal: To Be Published
Title: Thernary complexes of TCR P14 give insights into the mechanisms behind reestablishment of CTL responses against a viral escape mutant
Authors: Allerbring, E. / Duru, A. / Sun, R. / Han, X. / Uchtenhagen, H. / Madhurantakam, C. / Popov, A. / Markova, N. / Talyzina, A. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionOct 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
G: Protein Trav14-1,T-cell receptor alpha chain C region
H: T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region
P: LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND PF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9078
Polymers96,6305
Non-polymers2763
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-49 kcal/mol
Surface area37790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)255.110, 46.500, 89.020
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABGH

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 32087.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 13794.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein Protein Trav14-1,T-cell receptor alpha chain C region


Mass: 23072.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trav14-1, Tcra / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2JF94, UniProt: P01849
#4: Protein T-cell receptor beta chain V region C5,T-cell receptor beta-2 chain C region


Mass: 26647.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P04213, UniProt: P01851

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Protein/peptide , 1 types, 1 molecules P

#5: Protein/peptide LCMV-DERIVED GP33 ALTERED PEPTIDE LIGAND PF


Mass: 1027.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: KAPFNFATM / Source: (synth.) Lymphocytic choriomeningitis virus

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Non-polymers , 2 types, 395 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.75 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 19% PEG 6000, 0.1M Tris HCl pH 8.0 / PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.75→128 Å / Num. obs: 103816 / % possible obs: 98.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 5042 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s7u

1s7u


Resolution: 1.75→127.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.736 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21386 5198 5 %RANDOM
Rwork0.18794 ---
obs0.18926 98616 98.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å2-0 Å20.45 Å2
2---0.39 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.75→127.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6503 0 18 392 6913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196803
X-RAY DIFFRACTIONr_bond_other_d0.0020.026196
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9389243
X-RAY DIFFRACTIONr_angle_other_deg0.935314315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88723.894339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.506151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2051544
X-RAY DIFFRACTIONr_chiral_restr0.090.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217733
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021649
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_it1.042.0063254
X-RAY DIFFRACTIONr_mcbond_other1.042.0063253
X-RAY DIFFRACTIONr_mcangle_it1.75734063
X-RAY DIFFRACTIONr_mcangle_other1.75734064
X-RAY DIFFRACTIONr_scbond_it1.3532.1643549
X-RAY DIFFRACTIONr_scbond_other1.3382.1633549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1773.1775169
X-RAY DIFFRACTIONr_long_range_B_refined5.75516.3337504
X-RAY DIFFRACTIONr_long_range_B_other5.66815.9777379
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 390 -
Rwork0.289 7185 -
obs--96.77 %
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)
11.5127-0.1152-0.19131.48960.20921.1435-0.0306-0.01350.05820.00880.0187-0.03860.0175-0.04540.0120.07380.0046-0.01180.1370.02540.076265.246-24.19524.723
23.26991.0089-0.57491.46860.0531.396-0.0287-0.0753-0.03690.0365-0.00890.15660.077-0.18440.03760.03440.0548-0.00850.20320.00740.0788228.926-19.71331.502
32.9727-0.95190.73811.378-0.21751.53810.03170.294-0.0429-0.1456-0.05790.1519-0.0813-0.22020.02630.0322-0.0064-0.02940.23690.010.0291239.849-21.93911.811
43.623-0.6151-0.33260.45720.29120.1966-0.0312-0.64870.11950.03380.0831-0.08690.03320.0925-0.05190.01550.05930.00040.41090.04360.0394302.806-23.65430.614
54.84951.81750.34997.9677-2.80835.7492-0.4372-0.40890.30540.01320.1604-0.3237-0.47990.22160.27680.15850.0914-0.05030.1944-0.09190.104328.201-24.41925.5
61.3131-0.1819-0.18310.25610.18910.1725-0.00970.08710.02260.03750.02570.04280.0165-0.0047-0.0160.03160.02850.01450.19410.04830.0777300.128-26.7510.274
72.1068-0.90911.93712.0264-1.80493.65360.0255-0.0436-0.0652-0.03280.11930.0314-0.0079-0.0341-0.14480.04640.0381-0.00590.2029-0.00550.0652319.866-35.40112.476
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION2A182 - 276
3X-RAY DIFFRACTION3B2 - 99
4X-RAY DIFFRACTION4G10 - 147
5X-RAY DIFFRACTION5G148 - 196
6X-RAY DIFFRACTION6H1 - 142
7X-RAY DIFFRACTION7H143 - 237

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