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- PDB-4iiq: Crystal structure of a human MAIT TCR in complex with bovine MR1 -

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Basic information

Entry
Database: PDB / ID: 4iiq
TitleCrystal structure of a human MAIT TCR in complex with bovine MR1
Components
  • Beta-2-microglobulin, MHC class I-related protein
  • Human Mucosal Associated Invariant T cell receptor alpha chain
  • Human Mucosal Associated Invariant T cell receptor beta chain
KeywordsIMMUNE SYSTEM / MHC-class I / Immunoglobulin domain / Antigen presentation / Antigen recognition / Cell Membrane
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell receptor complex / Neutrophil degranulation / Translocation of ZAP-70 to Immunological synapse ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / DAP12 signaling / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell receptor complex / Neutrophil degranulation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / beta-2-microglobulin binding / T cell receptor binding / immunoglobulin complex, circulating / immunoglobulin 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 / antigen binding / response to bacterium / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / defense response to Gram-negative bacterium / adaptive immune response / blood microparticle / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Major histocompatibility complex class I-related gene protein / T cell receptor beta constant 1 / Beta-2-microglobulin / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsLopez-Sagaseta, J. / Adams, E.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: The molecular basis for Mucosal-Associated Invariant T cell recognition of MR1 proteins.
Authors: Lopez-Sagaseta, J. / Dulberger, C.L. / Crooks, J.E. / Parks, C.D. / Luoma, A.M. / McFedries, A. / Van Rhijn, I. / Saghatelian, A. / Adams, E.J.
History
DepositionDec 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Mucosal Associated Invariant T cell receptor alpha chain
B: Human Mucosal Associated Invariant T cell receptor beta chain
C: Beta-2-microglobulin, MHC class I-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8556
Polymers96,5663
Non-polymers2883
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.045, 87.410, 156.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Human Mucosal Associated Invariant T cell receptor alpha chain


Mass: 22851.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: Q6P4G7*PLUS
#2: Protein Human Mucosal Associated Invariant T cell receptor beta chain


Mass: 28291.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: Pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3)pLysS / References: UniProt: P01850*PLUS
#3: Protein Beta-2-microglobulin, MHC class I-related protein


Mass: 45423.613 Da / Num. of mol.: 1
Fragment: UNP C1ITJ8 residues 19-295, UNP P01888 residues 21-118
Source method: isolated from a genetically manipulated source
Details: Fusion Protein / Source: (gene. exp.) Bos taurus (cattle) / Gene: MR1, Bt.63045 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C1ITJ8, UniProt: P01888
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 1.5 M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 9, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 26556 / Num. obs: 26556 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 69.38 Å2 / Rsym value: 0.079 / Net I/σ(I): 14.63
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.72 / Rsym value: 0.681 / % possible all: 97.57

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→44.769 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.44 / σ(F): 1.35 / Phase error: 27.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1336 5.03 %
Rwork0.2134 --
obs0.2162 26550 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.9625 Å2
Refinement stepCycle: LAST / Resolution: 2.86→44.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6285 0 15 7 6307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046478
X-RAY DIFFRACTIONf_angle_d0.7548812
X-RAY DIFFRACTIONf_dihedral_angle_d14.0582273
X-RAY DIFFRACTIONf_chiral_restr0.055931
X-RAY DIFFRACTIONf_plane_restr0.0031147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.96180.40551130.33692414X-RAY DIFFRACTION98
2.9618-3.08040.33571340.28932505X-RAY DIFFRACTION100
3.0804-3.22050.34241450.26762477X-RAY DIFFRACTION100
3.2205-3.39030.31441240.23822513X-RAY DIFFRACTION100
3.3903-3.60260.29181320.21722508X-RAY DIFFRACTION100
3.6026-3.88060.25191520.20932493X-RAY DIFFRACTION100
3.8806-4.27080.24761330.19082525X-RAY DIFFRACTION100
4.2708-4.88820.21911350.15022537X-RAY DIFFRACTION100
4.8882-6.15610.22411570.18292552X-RAY DIFFRACTION100
6.1561-44.7690.25421110.20642690X-RAY DIFFRACTION98
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)
14.52781.13720.85826.7177-1.68554.46510.0608-0.0680.28170.27140.18570.2186-0.26910.0477-0.21420.3787-0.0077-0.11570.35110.00880.400428.364418.589433.9529
23.21371.67331.97585.1360.02655.9945-0.08330.1738-0.0754-0.1204-0.1805-0.1528-1.2651-0.12590.19620.6244-0.04720.03990.63-0.11040.470524.565946.590117.2691
30.30980.41790.77463.21291.29981.90010.3803-0.8968-0.5984-0.0898-0.02530.02270.57330.4476-0.30810.51120.1475-0.0450.851-0.02830.571925.474638.520616.6252
48.37316.17925.05197.6674.40366.191-0.411-0.76661.0645-0.6999-0.49640.4338-0.9652-0.56950.90950.82410.0115-0.00460.5626-0.10630.615920.643354.151318.1795
54.7253-0.85761.94284.4974-0.72583.57430.35210.1267-0.98540.06310.06650.5280.3823-0.4792-0.3270.4187-0.0753-0.21020.55810.09770.750312.27078.293419.1446
62.05-3.29822.55079.4983-1.59367.0681-0.2403-0.2832-0.4043-0.20030.01530.30471.0498-0.29670.09120.52690.0052-0.13040.39140.05280.652425.16025.398924.5651
72.58160.495-0.27745.1628-1.53055.60730.4139-0.10610.25870.11650.0580.5537-0.4883-0.1669-0.33530.51660.19580.00260.51-0.10570.26215.128737.27058.5231
86.1762.7876-0.47335.4887-0.05175.03090.1148-0.0628-0.2046-0.08520.05680.0309-0.09540.0382-0.23340.46430.0788-0.15370.51040.01450.297517.100334.56625.3463
91.1368-0.60090.17890.93820.02891.31790.3273-0.5645-0.14420.54810.12890.33010.5202-0.6252-0.26791.2621-0.22190.45480.52180.2450.636419.2771-36.059351.9331
101.99380.0381-0.00322.49810.15951.1168-0.28250.1056-0.1062-0.05850.30040.38871.0452-0.86520.01870.8293-0.28920.00360.65660.0990.47720.1919-35.357842.8208
110.78750.07290.19811.19650.07950.0785-0.32830.12250.13380.42370.1340.37241.1384-0.33620.00050.8718-0.08980.10160.51640.1340.413824.3218-24.736946.7354
122.5718-0.25220.013.0262-0.35491.8327-0.1745-0.0241-0.214-0.56070.17050.50010.2161-0.21930.01930.4579-0.1432-0.08960.44140.13110.442822.7238-13.434536.1614
132.50851.2098-0.1153.2583-0.95961.3437-0.5170.33980.2244-0.6511-0.0155-0.52910.30010.2655-0.01260.3761-0.0267-0.03070.52930.11350.537940.7985-11.682736.6025
140.2397-0.5337-0.20062.3917-0.34091.6464-0.12280.12410.36720.01110.16520.03230.1075-0.22070.03430.3167-0.0802-0.0450.45730.09540.455128.6221-5.356544.5933
152.5876-2.09440.62113.3651-1.08541.74490.26250.1963-0.3064-0.8893-0.1838-0.22770.58930.06330.00230.86030.10990.13250.50850.05920.412526.4609-34.770564.7296
160.80990.1743-0.17020.95230.19022.31970.14010.19010.063-0.4173-0.1899-0.16860.5490.3567-0.00990.72460.20340.18590.58460.03280.435630.7368-35.155766.3276
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 201 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 94 )
6X-RAY DIFFRACTION6chain 'B' and (resid 95 through 109 )
7X-RAY DIFFRACTION7chain 'B' and (resid 110 through 140 )
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 244 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 22 )
10X-RAY DIFFRACTION10chain 'C' and (resid 23 through 89 )
11X-RAY DIFFRACTION11chain 'C' and (resid 90 through 125 )
12X-RAY DIFFRACTION12chain 'C' and (resid 126 through 227 )
13X-RAY DIFFRACTION13chain 'C' and (resid 228 through 248 )
14X-RAY DIFFRACTION14chain 'C' and (resid 249 through 295 )
15X-RAY DIFFRACTION15chain 'C' and (resid 296 through 329 )
16X-RAY DIFFRACTION16chain 'C' and (resid 330 through 385 )

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