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- PDB-4lcc: Crystal structure of a human MAIT TCR in complex with a bacterial... -

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Basic information

Entry
Database: PDB / ID: 4lcc
TitleCrystal structure of a human MAIT TCR in complex with a bacterial antigen bound to humanized bovine MR1
Components
  • (Human MAIT TCR ...) x 2
  • Beta-2-microglobulin, MHC class I-related protein
KeywordsIMMUNE SYSTEM / Immunoglobulin domain / MHC-class I-like / Antigen presentation / Antigen recognition / B Vitamins metabolites / 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 / alpha-beta T cell receptor complex / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse ...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 / alpha-beta T cell receptor complex / Neutrophil degranulation / antigen processing and presentation of peptide antigen via MHC class I / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / beta-2-microglobulin binding / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / T cell receptor binding / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class II protein complex binding / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / T cell differentiation in thymus / early endosome membrane / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / endoplasmic reticulum membrane / extracellular space / 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 ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1XL / 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 (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 3.263 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 21, 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)97,4348
Polymers96,7223
Non-polymers7135
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-80 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.902, 88.585, 155.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 45265.551 Da / Num. of mol.: 1 / Fragment: P01888 residues 21-118, C1ITJ8 residues 19-295 / Mutation: A185M, R260Q, Q264L
Source method: isolated from a genetically manipulated source
Details: Fusion Protein / Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: MR1, Bt.63045 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C1ITJ8, UniProt: P01888

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Human MAIT TCR ... , 2 types, 2 molecules AB

#2: Protein Human MAIT TCR alpha chain


Mass: 23164.713 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: 28291.428 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 / References: UniProt: P01850*PLUS

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Non-polymers , 3 types, 6 molecules

#4: Chemical ChemComp-1XL / 1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-arabinitol


Mass: 328.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N4O7
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: 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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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: 3.06 Å3/Da / Density % sol: 59.79 %
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 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 3.263→50 Å / Num. all: 18509 / Num. obs: 18509 / % possible obs: 97.04 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 89.8 Å2 / Net I/σ(I): 12.8
Reflection shellResolution: 3.263→3.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 3.92 / Num. unique all: 766 / % possible all: 78.3

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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: 3.263→48.316 Å / SU ML: 0.54 / σ(F): 1.36 / Phase error: 31.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3124 938 5.07 %
Rwork0.2569 --
obs0.2597 18496 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.263→48.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 43 1 5827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065986
X-RAY DIFFRACTIONf_angle_d1.048142
X-RAY DIFFRACTIONf_dihedral_angle_d13.9832076
X-RAY DIFFRACTIONf_chiral_restr0.069867
X-RAY DIFFRACTIONf_plane_restr0.0051044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.263-3.43510.34921080.31062062X-RAY DIFFRACTION81
3.4351-3.65020.37761260.28642476X-RAY DIFFRACTION97
3.6502-3.9320.31391540.27782535X-RAY DIFFRACTION100
3.932-4.32740.32671400.24232553X-RAY DIFFRACTION100
4.3274-4.95310.25741360.19942591X-RAY DIFFRACTION100
4.9531-6.23820.28311600.24862581X-RAY DIFFRACTION100
6.2382-48.3160.32231140.26452760X-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)
13.80010.03030.3836.2436-0.28283.3379-0.066-0.18550.61870.8141-0.35210.2172-1.6162-0.64470.44431.56060.11520.08470.66540.03930.66-21.916234.123833.7299
22.1858-0.238-0.68885.3741-2.91164.169-0.097-0.2722-0.09730.808-0.1049-0.0434-2.01350.2370.11890.9316-0.14780.02880.68330.16680.6604-13.928512.254940.4703
30.6171-0.2796-0.50414.1811-4.22124.6275-0.0234-0.08260.03430.25260.0002-0.2257-0.76420.03580.1311.0372-0.1094-0.09020.55160.00710.5681-16.225528.822714.7382
44.07861.7054-1.81883.41141.32083.77120.12580.0079-0.1841-0.075-0.0638-0.13650.57480.2445-0.05770.65280.111-0.02860.52670.14670.5449-11.7575-18.611743.8511
51.2506-0.4402-0.26612.1412-0.63463.1653-0.6453-0.47920.33210.0561-0.0128-0.15951.54520.64910.66551.59550.1972-0.11540.67450.06770.7104-13.9771-45.944763.0883
60.36060.3113-0.81280.4437-0.93692.62590.0807-0.14580.21220.7304-0.13640.01580.6189-0.57690.19791.37860.2376-0.03520.8626-0.18580.9234-19.5848-49.193160.2377
78.06861.1253-6.21230.3219-1.15315.4517-0.58070.51430.38220.698-0.15790.26590.3783-0.48230.41940.95540.0107-0.1140.65590.00010.665-20.3858-44.783561.4581
83.90690.6517-1.41514.6718-0.35794.80330.2983-0.07980.6645-0.05310.03060.8199-0.763-0.9664-0.29480.65580.1340.090.74520.22470.7731-29.1488-8.581458.2082
94.02420.04220.84542.39671.69553.4669-1.01080.5923-0.0033-0.94350.70940.1220.8717-0.88890.11910.5039-0.06820.03390.76890.16660.6204-26.5831-15.484859.1147
106.9636-1.8219-1.62265.09271.47645.2547-0.44230.1788-0.16340.71650.2718-0.66651.0514-0.06290.20230.8634-0.03650.07950.50060.05070.4337-18.409-41.150870.8505
113.6844-0.093-1.19275.266-0.03711.78180.19621.00160.7689-0.7725-0.39530.17930.3917-0.45920.15950.4844-0.19190.01540.9637-0.00450.7428-23.672-35.46264.8275
125.1388-2.7205-1.09775.13130.89374.7843-0.4660.06480.29382.22680.0366-0.01581.2472-0.11650.04541.0422-0.26430.04190.58490.04430.575-21.5374-35.442976.0439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'C' and (resid 91 through 272 )
3X-RAY DIFFRACTION3chain 'C' and (resid 273 through 384 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 129 )
6X-RAY DIFFRACTION6chain 'A' and (resid 130 through 151 )
7X-RAY DIFFRACTION7chain 'A' and (resid 152 through 177 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 124 )
10X-RAY DIFFRACTION10chain 'B' and (resid 125 through 162 )
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 188 )
12X-RAY DIFFRACTION12chain 'B' and (resid 189 through 244 )

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