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- PDB-4l9l: Crystal structure of a human Valpha7.2/Vbeta13.2 MAIT TCR in comp... -

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Basic information

Entry
Database: PDB / ID: 4l9l
TitleCrystal structure of a human Valpha7.2/Vbeta13.2 MAIT TCR in complex with bovine MR1
Components
  • Beta-2-microglobulin, MHC class I-related protein
  • Human MAIT TCR alpha chain
  • Human MAIT TCR beta chain
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / MHC-class I-like / Antigen presentation / Antigen recognition / Vitamin metabolites / 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 speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.4 Å
AuthorsLopez-Sagaseta, J. / Adams, E.J.
CitationJournal: J.Immunol. / Year: 2013
Title: MAIT Recognition of a Stimulatory Bacterial Antigen Bound to MR1.
Authors: Lopez-Sagaseta, J. / Dulberger, C.L. / McFedries, A. / Cushman, M. / Saghatelian, A. / Adams, E.J.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-2-microglobulin, MHC class I-related protein
A: Human MAIT TCR alpha chain
B: Human MAIT TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9165
Polymers96,7243
Non-polymers1922
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-2-microglobulin, MHC class I-related protein

A: Human MAIT TCR alpha chain
B: Human MAIT TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9165
Polymers96,7243
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
crystal symmetry operation2_554-x+1/2,-y,z-1/21
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-59 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.767, 86.980, 156.345
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-2-microglobulin, MHC class I-related protein


Mass: 45423.613 Da / Num. of mol.: 1
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
#2: Protein Human MAIT TCR alpha chain


Mass: 23146.674 Da / Num. of mol.: 1 / Mutation: T157C
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
#3: Protein Human MAIT TCR beta chain


Mass: 28153.426 Da / Num. of mol.: 1 / Mutation: S179C
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 1.6 M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: MAR 300 CCD / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 15806 / Num. obs: 15806 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 89.38 Å2 / Net I/σ(I): 14.8
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 5.4 / Num. unique all: 742 / % possible all: 95.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementResolution: 3.4→47.58 Å / SU ML: 0.53 / σ(F): 1.35 / Phase error: 32.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.312 805 5.1 %
Rwork0.254 --
obs0.257 15779 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.32 Å2
Refinement stepCycle: LAST / Resolution: 3.4→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 10 1 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056218
X-RAY DIFFRACTIONf_angle_d0.8978454
X-RAY DIFFRACTIONf_dihedral_angle_d14.2512172
X-RAY DIFFRACTIONf_chiral_restr0.058893
X-RAY DIFFRACTIONf_plane_restr0.0041092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.60530.36561180.30232170X-RAY DIFFRACTION86
3.6053-3.88360.34241470.28452455X-RAY DIFFRACTION98
3.8836-4.27420.33261330.25722521X-RAY DIFFRACTION99
4.2742-4.89210.25391360.212541X-RAY DIFFRACTION100
4.8921-6.16150.28651560.23922554X-RAY DIFFRACTION100
6.1615-47.580.31741150.2482733X-RAY DIFFRACTION100
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)
12.845-0.89820.99484.8015-0.53033.95920.0366-0.13450.3750.52960.1720.3271-0.32620.1717-0.17810.7837-0.113-0.16140.33430.06950.481129.045418.868834.0883
26.9266-1.32892.08655.926-2.11331.4589-0.88330.1555-0.03870.30230.0487-0.0472-0.87640.10840.8040.9846-0.22190.01580.9253-0.14940.553925.076246.696517.5393
31.2886-1.1942-0.15871.10780.15890.0111-0.2313-0.1617-0.5080.23050.1409-0.410.1320.40280.05320.04140.2163-0.22541.0571-0.00011.224226.120238.790516.6928
45.90486.21966.47967.77825.44898.5914-0.8009-0.64551.92160.899-0.32021.4959-2.4094-1.52170.76411.05050.15560.11370.8672-0.12121.31620.931954.226818.4039
50.6172-0.210.41514.55480.05893.52920.67040.1239-0.10360.95040.01980.2086-0.0122-1.0382-0.21920.5286-0.1658-0.29550.98130.24530.902913.730310.482419.1246
61.2738-0.70870.20984.86-0.40433.04640.3185-0.3925-0.66460.49770.25720.2183-0.4531-0.6773-0.14920.5868-0.2071-0.37310.93090.06980.71614.996317.166817.2283
79.86290.0871-3.07334.52360.48456.7601-0.4121-1.4219-0.8844-0.643-0.38180.1212-0.06450.28420.52410.78130.2249-0.18470.71640.03840.558718.126735.071410.3512
81.76730.20251.15173.64360.22765.1128-0.10160.1891-0.2228-0.81290.23470.18320.03930.2246-0.040.58230.0459-0.18410.84040.00050.523117.451234.88581.5165
92.36621.0023-0.64225.4037-0.8221.244-0.55460.39350.244-0.64410.39860.26541.1226-0.34650.12971.3455-0.2119-0.22430.66540.14460.562426.4918-17.783139.2899
100.45060.9418-0.40374.3331-2.63351.67180.1193-0.16390.40060.9715-0.1391.09330.1144-0.5823-0.52170.6190.00830.20370.708-0.02430.730519.9355-8.529355.8448
111.65810.59490.13112.8473-3.40014.48430.2249-0.1745-0.1993-0.8088-0.3092-0.47190.71270.42880.32941.01130.28540.20770.66840.02430.562929.0904-34.936565.9074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:103 )A3 - 103
2X-RAY DIFFRACTION2( CHAIN A AND RESID 104:150 )A104 - 150
3X-RAY DIFFRACTION3( CHAIN A AND RESID 151:170 )A151 - 170
4X-RAY DIFFRACTION4( CHAIN A AND RESID 171:201 )A171 - 201
5X-RAY DIFFRACTION5( CHAIN B AND RESID 2:47 )B2 - 47
6X-RAY DIFFRACTION6( CHAIN B AND RESID 48:147 )B48 - 147
7X-RAY DIFFRACTION7( CHAIN B AND RESID 148:195 )B148 - 195
8X-RAY DIFFRACTION8( CHAIN B AND RESID 196:251 )B196 - 251
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:271 )C1 - 271
10X-RAY DIFFRACTION10( CHAIN C AND RESID 272:295 )C272 - 295
11X-RAY DIFFRACTION11( CHAIN C AND RESID 296:385 )C296 - 385

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