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- PDB-7ufj: Structure of human MR1-ethylvanillin in complex with human MAIT A... -

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Basic information

Entry
Database: PDB / ID: 7ufj
TitleStructure of human MR1-ethylvanillin in complex with human MAIT A-F7 TCR
Components
  • (MAIT T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / ANTIGEN PRESENTATION / T-CELL RECEPTOR / 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 / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / 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 ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / 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 / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / 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 / 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
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 / 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 / : ...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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 3-ethoxy-4-hydroxybenzaldehyde / PROLINE / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWang, C.J. / Rossjohn, J. / Le Nours, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Quantitative affinity measurement of small molecule ligand binding to Major Histocompatibility Complex class-I related protein 1 MR1.
Authors: Wang, C.J.H. / Awad, W. / Liu, L. / Mak, J.Y.W. / Veerapen, N. / Illing, P.T. / Purcell, A.W. / Eckle, S.B.G. / McCluskey, J. / Besra, G.S. / Fairlie, D.P. / Rossjohn, J. / Le Nours, J.
History
DepositionMar 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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

Downloads & links

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Assembly

Deposited unit
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
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,57129
Polymers187,5758
Non-polymers1,99621
Water6,828379
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)94,62212
Polymers93,7884
Non-polymers8348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Major histocompatibility complex class I-related gene protein
D: Beta-2-microglobulin
E: MAIT T-cell receptor alpha chain
F: MAIT T-cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,95017
Polymers93,7884
Non-polymers1,16213
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)217.936, 70.888, 144.387
Angle α, β, γ (deg.)90.000, 104.861, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 31711.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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

#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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)

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Non-polymers , 5 types, 400 molecules

#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical ChemComp-N36 / 3-ethoxy-4-hydroxybenzaldehyde / Ethyl vanillin


Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: BTP PEG 3350 NaAc / PH range: 6.1 - 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→48.43 Å / Num. obs: 73277 / % possible obs: 98.76 % / Redundancy: 2 % / Biso Wilson estimate: 42.17 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.05929 / Rpim(I) all: 0.05929 / Rrim(I) all: 0.08385 / Net I/σ(I): 9.24
Reflection shellResolution: 2.5→2.589 Å / Rmerge(I) obs: 0.4452 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 7243 / CC1/2: 0.679 / Rpim(I) all: 0.4452 / Rrim(I) all: 0.6296

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.18.2_3874phasing
Aimlessdata scaling
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U2V

5u2v


Resolution: 2.5→48.43 Å / SU ML: 0.3123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 3724 5.08 %
Rwork0.1805 69529 -
obs0.1833 73253 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 130 379 13099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008113103
X-RAY DIFFRACTIONf_angle_d0.998517811
X-RAY DIFFRACTIONf_chiral_restr0.0541893
X-RAY DIFFRACTIONf_plane_restr0.00672303
X-RAY DIFFRACTIONf_dihedral_angle_d17.55464610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.33971180.27852603X-RAY DIFFRACTION98.62
2.53-2.560.35981340.26272521X-RAY DIFFRACTION98.66
2.56-2.60.33291210.24042593X-RAY DIFFRACTION98.73
2.6-2.640.29851450.23982538X-RAY DIFFRACTION98.86
2.64-2.680.28581380.22632550X-RAY DIFFRACTION98.93
2.68-2.720.28141540.22522579X-RAY DIFFRACTION98.91
2.72-2.760.30081360.21892496X-RAY DIFFRACTION98.8
2.76-2.810.25861630.21622567X-RAY DIFFRACTION98.88
2.81-2.860.30411420.22472558X-RAY DIFFRACTION99.08
2.86-2.920.32131350.22222571X-RAY DIFFRACTION98.8
2.92-2.980.32971450.21342561X-RAY DIFFRACTION99.16
2.98-3.040.26991450.21052532X-RAY DIFFRACTION99.04
3.04-3.110.27021340.19872598X-RAY DIFFRACTION99.2
3.11-3.190.26921340.19752563X-RAY DIFFRACTION99.15
3.19-3.280.26811570.20392566X-RAY DIFFRACTION99.02
3.28-3.370.24071430.18972605X-RAY DIFFRACTION99.06
3.37-3.480.21361510.17792518X-RAY DIFFRACTION99.04
3.48-3.610.26231390.17882570X-RAY DIFFRACTION99.09
3.61-3.750.24131520.17372573X-RAY DIFFRACTION98.91
3.75-3.920.20651250.172605X-RAY DIFFRACTION98.34
3.92-4.130.22531230.15982582X-RAY DIFFRACTION98.29
4.13-4.390.1921280.14022555X-RAY DIFFRACTION98.24
4.39-4.720.16941420.13432606X-RAY DIFFRACTION98.99
4.72-5.20.2031250.14152613X-RAY DIFFRACTION98.84
5.2-5.950.20511200.17292630X-RAY DIFFRACTION99.21
5.95-7.490.20851510.1822596X-RAY DIFFRACTION98.46
7.49-48.430.18861240.15992680X-RAY DIFFRACTION97.06

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