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- PDB-8vz8: Crystal structure of mouse MAIT M2B TCR-MR1-5-OP-RU complex -

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Basic information

Entry
Database: PDB / ID: 8vz8
TitleCrystal structure of mouse MAIT M2B TCR-MR1-5-OP-RU complex
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • Mouse MAIT MBV13-2B b-chain
  • Mouse MAIT TRAV1-TRAJ33 a-chain
KeywordsIMMUNE SYSTEM / Mouse MAIT TCR recognition of MR1
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 / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / late endosome membrane / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / Golgi membrane / external side of plasma membrane / innate immune response / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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
Similarity search - Domain/homology
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsCiacchi, L. / Rossjohn, J. / Awad, W.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE220101491 Australia
Australian Research Council (ARC)DP220102401 Australia
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Mouse mucosal-associated invariant T cell receptor recognition of MR1 presenting the vitamin B metabolite, 5-(2-oxopropylideneamino)-6-d-ribitylaminouracil.
Authors: Ciacchi, L. / Mak, J.Y.W. / Le, J.P. / Fairlie, D.P. / McCluskey, J. / Corbett, A.J. / Rossjohn, J. / Awad, W.
History
DepositionFeb 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
C: Mouse MAIT TRAV1-TRAJ33 a-chain
D: Mouse MAIT MBV13-2B b-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6686
Polymers93,2604
Non-polymers4082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-46 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.486, 84.635, 166.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 31709.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mr1, Mr1a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8HWB0
#2: Protein Beta-2-microglobulin


Mass: 11731.427 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein Mouse MAIT TRAV1-TRAJ33 a-chain


Mass: 22650.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein Mouse MAIT MBV13-2B b-chain


Mass: 27168.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris Propane (pH 7.5 - 8.5), 16-22% PEG 3350 and 0.2M sodium acetate
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 3.45→43.64 Å / Num. obs: 12522 / % possible obs: 99.77 % / Redundancy: 4.29 % / CC1/2: 0.977 / Net I/σ(I): 4.29
Reflection shellResolution: 3.45→3.57 Å / Num. unique obs: 1235 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→43.64 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 1253 10.01 %
Rwork0.2561 --
obs0.2585 12516 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 28 0 5812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035986
X-RAY DIFFRACTIONf_angle_d0.5778203
X-RAY DIFFRACTIONf_dihedral_angle_d14.6151975
X-RAY DIFFRACTIONf_chiral_restr0.043921
X-RAY DIFFRACTIONf_plane_restr0.0061059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.590.33331380.31181240X-RAY DIFFRACTION100
3.59-3.750.34661340.2921204X-RAY DIFFRACTION100
3.75-3.950.30471370.2891240X-RAY DIFFRACTION100
3.95-4.20.31041360.26151222X-RAY DIFFRACTION100
4.2-4.520.25811370.2361233X-RAY DIFFRACTION99
4.52-4.970.20651400.21281255X-RAY DIFFRACTION100
4.97-5.690.29131390.23931247X-RAY DIFFRACTION100
5.69-7.170.30421420.2781279X-RAY DIFFRACTION100
7.17-43.640.26161500.24441343X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 10.3971 Å / Origin y: -21.7412 Å / Origin z: 7.8189 Å
111213212223313233
T0.3297 Å20.0223 Å20.0629 Å2-0.1943 Å2-0.0652 Å2--0.3059 Å2
L1.4138 °20.3351 °2-0.5517 °2--0.2102 °2-0.0977 °2--1.0344 °2
S0.2129 Å °-0.0361 Å °0.2214 Å °0.011 Å °-0.0658 Å °-0.0407 Å °0.0414 Å °-0.0521 Å °0.0085 Å °
Refinement TLS groupSelection details: all

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