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- PDB-4l8s: Crystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in comp... -

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Basic information

Entry
Database: PDB / ID: 4l8s
TitleCrystal structure of a human Valpha7.2/Vbeta13.3 MAIT TCR in complex with bovine MR1
Components
  • Beta-2-microglobulin, MHC class I-related protein
  • Muccosal Associated Invariant T Cell Receptor alpha chain
  • Muccosal Associated Invariant T Cell Receptor beta chain
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / MHC-class I / Antigen presentation / Antigen recognition / Antigen / Cell membrane
Function / homology
Function and homology information


ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / Neutrophil degranulation / beta-2-microglobulin binding / T cell receptor binding ...ER-Phagosome pathway / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / Neutrophil degranulation / beta-2-microglobulin binding / T cell receptor binding / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / T cell differentiation in thymus / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / endoplasmic reticulum membrane / extracellular space / extracellular region / 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 / : ...: / 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 subtype / Immunoglobulin / 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 / 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 / Beta-2-microglobulin / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.9 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 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Muccosal Associated Invariant T Cell Receptor alpha chain
B: Muccosal 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)97,2918
Polymers96,8113
Non-polymers4805
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.068, 87.285, 155.817
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 Muccosal Associated Invariant T Cell Receptor alpha chain


Mass: 23154.676 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
#2: Protein Muccosal Associated Invariant T Cell Receptor beta chain


Mass: 28232.311 Da / Num. of mol.: 1 / Mutation: S172C
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
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 1.7 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: MARMOSAIC 300 mm 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: 2.9→50 Å / Num. all: 27400 / Num. obs: 27400 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 71.9 Å2 / Net I/σ(I): 20.9
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1223 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementResolution: 2.9→44.039 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1251 5.06 %
Rwork0.228 --
obs0.2305 24717 95.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 25 7 6344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036520
X-RAY DIFFRACTIONf_angle_d0.758882
X-RAY DIFFRACTIONf_dihedral_angle_d12.1512262
X-RAY DIFFRACTIONf_chiral_restr0.056941
X-RAY DIFFRACTIONf_plane_restr0.0031157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0150.35811180.33482567X-RAY DIFFRACTION95
3.015-3.15220.36021520.29972591X-RAY DIFFRACTION97
3.1522-3.31830.35591380.28552610X-RAY DIFFRACTION97
3.3183-3.52610.30921390.24722623X-RAY DIFFRACTION97
3.5261-3.79820.3091480.232620X-RAY DIFFRACTION97
3.7982-4.18020.23911540.20082590X-RAY DIFFRACTION96
4.1802-4.78440.18771370.16312623X-RAY DIFFRACTION96
4.7844-6.02540.22831560.19322604X-RAY DIFFRACTION95
6.0254-44.0390.3051090.22382638X-RAY DIFFRACTION90
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)
10.5264-0.84081.1257.3769-3.13133.55920.0543-0.0852-0.08880.51790.11-0.1513-0.27750.1128-0.15210.418-0.0595-0.08380.45130.01050.478928.419225.396929.5479
25.92532.55865.38395.6541-0.60046.97960.3509-0.9506-0.60550.573-0.2171-0.31880.2378-0.1457-0.01670.64120.03660.00190.7680.06730.482425.464242.19819.328
37.57895.99237.73237.5075.35598.6255-0.8192-0.67631.1151-0.978-0.16440.4162-1.2024-0.97871.03831.05060.03940.03440.6207-0.12090.633321.091254.355818.2201
42.9165-0.67181.43864.8429-1.5644.37790.230.168-0.52110.06690.27840.49080.5578-0.5509-0.54380.4544-0.1086-0.21020.58120.15050.705112.60488.716519.8079
51.9256-0.44810.77785.3352-2.00874.1903-0.0174-0.3189-0.62780.34050.41680.39950.1235-0.7968-0.34210.5322-0.0381-0.11220.57250.07390.498214.617416.450217.752
67.45713.8796-0.61246.39340.24025.23250.2115-0.3921-0.2759-0.05190.0053-0.092-0.32680.301-0.22310.48270.1046-0.13180.53990.01420.310618.982736.61945.6291
72.05250.72510.05076.1636-1.35932.908-0.34580.0805-0.01620.04640.35670.36470.6221-0.37210.00580.6688-0.124-0.02270.47020.08780.396225.5455-20.217639.9151
80.93130.54640.62373.3062-3.87176.1896-0.1338-0.0832-0.1094-0.26270.2516-0.16730.43810.00030.02680.82870.13920.17120.53080.00490.429127.5052-29.538363.2881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:135 )A3 - 135
2X-RAY DIFFRACTION2( CHAIN A AND RESID 136:169 )A136 - 169
3X-RAY DIFFRACTION3( CHAIN A AND RESID 170:200 )A170 - 200
4X-RAY DIFFRACTION4( CHAIN B AND RESID 2:94 )B2 - 94
5X-RAY DIFFRACTION5( CHAIN B AND RESID 95:123 )B95 - 123
6X-RAY DIFFRACTION6( CHAIN B AND RESID 124:243 )B124 - 243
7X-RAY DIFFRACTION7( CHAIN C AND RESID 1:272 )C1 - 272
8X-RAY DIFFRACTION8( CHAIN C AND RESID 273:386 )C273 - 386

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