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- PDB-4l4v: Structure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH -

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Basic information

Entry
Database: PDB / ID: 4l4v
TitleStructure of human MAIT TCR in complex with human MR1-RL-6-Me-7-OH
Components
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsMembrane Protein/Immune System / MHC Class I-related protein / MAIT TCR / Immune System / Vitamin B metabolites / Membrane Protein-Immune System complex
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell activation / Generation of second messenger molecules ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
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/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
Chem-1VY / T cell receptor beta constant 1 / Beta-2-microglobulin / TRA@ protein / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.9 Å
AuthorsPatel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B.G. / Birkinshaw, R.W. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. ...Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B.G. / Birkinshaw, R.W. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / Sullivan, L.C. / Brooks, A.G. / Chen, Z. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2013
Title: Recognition of vitamin B metabolites by mucosal-associated invariant T cells.
Authors: Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B. / Birkinshaw, R. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / ...Authors: Patel, O. / Kjer-Nielsen, L. / Le Nours, J. / Eckle, S.B. / Birkinshaw, R. / Beddoe, T. / Corbett, A.J. / Liu, L. / Miles, J.J. / Meehan, B. / Reantragoon, R. / Sandoval-Romero, M.L. / Sullivan, L.C. / Brooks, A.G. / Chen, Z. / Fairlie, D.P. / McCluskey, J. / Rossjohn, J.
History
DepositionJun 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.3Nov 20, 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: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related gene protein
D: MAIT T-cell receptor alpha chain
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,24613
Polymers187,3138
Non-polymers9335
Water19,8531102
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
G: MAIT T-cell receptor alpha chain
H: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1697
Polymers93,6564
Non-polymers5123
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: MAIT T-cell receptor alpha chain
E: MAIT T-cell receptor beta chain
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0776
Polymers93,6564
Non-polymers4202
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)218.370, 71.203, 144.642
Angle α, β, γ (deg.)90.00, 104.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBF

#1: Protein Major histocompatibility complex class I-related gene protein


Mass: 31711.670 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 23-292 / Mutation: C261S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769

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MAIT T-cell receptor ... , 2 types, 4 molecules DGEH

#3: Protein MAIT T-cell receptor alpha chain


Mass: 22650.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR alpha / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6P4G7*PLUS
#4: Protein MAIT T-cell receptor beta chain


Mass: 27546.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCR beta / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01850*PLUS

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Non-polymers , 3 types, 1107 molecules

#5: Chemical ChemComp-1VY / 1-deoxy-1-(7-hydroxy-6-methyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol


Mass: 328.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N4O7
#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.: 1102 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→75.44 Å / Num. all: 169283 / Num. obs: 168903 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 23.62 Å2 / Rmerge(I) obs: 0.189 / Net I/σ(I): 9.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 2.2 / Num. unique all: 24566 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: PHASER
Starting model: PDB entry 4GUP

4gup


Resolution: 1.9→40.45 Å / Cor.coef. Fo:Fc: 0.9459 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 8503 5.03 %RANDOM
Rwork0.1775 ---
all0.179 168903 --
obs0.179 168898 99.79 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.5088 Å20 Å20.6683 Å2
2---5.4688 Å20 Å2
3---2.96 Å2
Refine analyzeLuzzati coordinate error obs: 0.202 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12477 0 64 1102 13643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112952HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0317651HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5771SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes302HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1899HARMONIC5
X-RAY DIFFRACTIONt_it12952HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1666SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14700SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2297 615 4.94 %
Rwork0.2132 11846 -
all0.214 12461 -
obs--99.79 %

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