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- PDB-9y0t: Crystal structure of human MAIT A-F7 TCR-MR1*02-5-OP-RU complex -

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Basic information

Entry
Database: PDB / ID: 9y0t
TitleCrystal structure of human MAIT A-F7 TCR-MR1*02-5-OP-RU complex
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related protein 1
  • TCR alpha chain
  • TCR beta chain
KeywordsIMMUNE SYSTEM / MAIT TCR / MR1 / metabolite presentation
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 / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway ...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 / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal 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 exosome / extracellular region / membrane / identical protein binding / 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
ACETATE ION / Chem-Q87 / 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: 2.3 Å
AuthorsLetoga, V. / Rossjohn, J. / Awad, W.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE220101491 Australia
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Allelic variation alters expression and antigen presentation of MR1 allomorphs.
Authors: Nelson, A.G. / Letoga, V. / Lee, C.Z.Q. / Samer, C. / Li, S. / Meehan, L.J. / McWilliam, H.E.G. / Gherardin, N.A. / Abendroth, A. / Villadangos, J.A. / Slobedman, B. / Corbett, A.J. / ...Authors: Nelson, A.G. / Letoga, V. / Lee, C.Z.Q. / Samer, C. / Li, S. / Meehan, L.J. / McWilliam, H.E.G. / Gherardin, N.A. / Abendroth, A. / Villadangos, J.A. / Slobedman, B. / Corbett, A.J. / McCluskey, J. / Rossjohn, J. / Chen, Z. / Souter, M.N.T. / Awad, W.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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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 protein 1
B: Beta-2-microglobulin
C: Major histocompatibility complex class I-related protein 1
D: TCR alpha chain
E: TCR beta chain
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,12316
Polymers188,1388
Non-polymers9858
Water15,187843
1
C: Major histocompatibility complex class I-related protein 1
F: Beta-2-microglobulin
G: TCR alpha chain
H: TCR beta chain
hetero molecules

A: Major histocompatibility complex class I-related protein 1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,66414
Polymers137,6796
Non-polymers9858
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_548-x+1/2,y-1/2,-z+31
Buried area13720 Å2
ΔGint-94 kcal/mol
Surface area53390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.226, 71.054, 144.176
Angle α, β, γ (deg.)90.000, 104.573, 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 , 4 types, 8 molecules ACBFDGEH

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


Mass: 31730.717 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 (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein TCR alpha chain


Mass: 22781.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein TCR beta chain


Mass: 27677.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 851 molecules

#5: Chemical ChemComp-Q87 / 1-deoxy-1-({2,6-dioxo-5-[(E)-(2-oxopropylidene)amino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol


Mass: 330.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N4O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, BTP, Cacl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→46.62 Å / Num. obs: 94639 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 42.85 Å2 / CC1/2: 0.997 / Net I/σ(I): 10
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 4603 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.62 Å / SU ML: 0.3061 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 4717 4.99 %
Rwork0.191 89872 -
obs0.1923 94589 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.67 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12661 0 63 843 13567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001813289
X-RAY DIFFRACTIONf_angle_d0.527218109
X-RAY DIFFRACTIONf_chiral_restr0.04271933
X-RAY DIFFRACTIONf_plane_restr0.00382371
X-RAY DIFFRACTIONf_dihedral_angle_d13.07744738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.36721500.30152926X-RAY DIFFRACTION98.87
2.33-2.350.34861610.29912957X-RAY DIFFRACTION98.76
2.35-2.380.27851640.27272951X-RAY DIFFRACTION98.83
2.38-2.410.30231410.26582935X-RAY DIFFRACTION98.72
2.41-2.440.33311860.26143021X-RAY DIFFRACTION99.04
2.44-2.480.28631540.26252905X-RAY DIFFRACTION98.96
2.48-2.510.32111350.26382994X-RAY DIFFRACTION98.71
2.51-2.550.25531470.25133019X-RAY DIFFRACTION98.91
2.55-2.590.2991530.24242941X-RAY DIFFRACTION99.07
2.59-2.630.28221490.24713022X-RAY DIFFRACTION99.19
2.63-2.680.30461680.24082945X-RAY DIFFRACTION99.23
2.68-2.730.24591660.2453024X-RAY DIFFRACTION99.35
2.73-2.780.29661420.25162958X-RAY DIFFRACTION99.61
2.78-2.840.29371720.25382984X-RAY DIFFRACTION99.56
2.84-2.90.27621630.2262963X-RAY DIFFRACTION99.65
2.9-2.970.23641660.22663030X-RAY DIFFRACTION99.53
2.97-3.040.22511550.21262968X-RAY DIFFRACTION99.52
3.04-3.120.24461650.2073011X-RAY DIFFRACTION99.69
3.12-3.210.2371520.20693019X-RAY DIFFRACTION99.65
3.21-3.320.24431440.2032978X-RAY DIFFRACTION99.3
3.32-3.440.2091600.19453002X-RAY DIFFRACTION99.47
3.44-3.570.19541690.183021X-RAY DIFFRACTION99.72
3.57-3.740.20851650.16553016X-RAY DIFFRACTION99.41
3.74-3.930.1971490.16693010X-RAY DIFFRACTION99.59
3.93-4.180.17011440.15513020X-RAY DIFFRACTION99.28
4.18-4.50.13611670.13163013X-RAY DIFFRACTION99.41
4.5-4.950.15221550.12853014X-RAY DIFFRACTION99.34
4.95-5.670.19551510.15243048X-RAY DIFFRACTION99.29
5.67-7.140.21041720.18643041X-RAY DIFFRACTION98.71
7.14-46.620.19371520.18683136X-RAY DIFFRACTION98.77
Refinement TLS params.Method: refined / Origin x: 22.4367003259 Å / Origin y: 64.9366700255 Å / Origin z: 189.567526828 Å
111213212223313233
T0.270998252385 Å2-0.0257333591439 Å20.0197474790649 Å2-0.235062625937 Å20.03997674927 Å2--0.266533993084 Å2
L0.261054183025 °2-0.0409945553967 °20.254787126501 °2-0.205316291848 °20.102419364942 °2--0.761631540339 °2
S-0.0154316922241 Å °0.0729804654644 Å °0.0143258285223 Å °-0.0429813742499 Å °0.0106868364901 Å °-0.0332213609483 Å °0.025586967469 Å °0.186652932282 Å °0.00314083041046 Å °
Refinement TLS groupSelection details: all

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