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- PDB-26sj: Crystal structure of MAIT A-F7 TCR-MR1-xanthine -

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Basic information

Entry
Database: PDB / ID: 26sj
TitleCrystal structure of MAIT A-F7 TCR-MR1-xanthine
Components
  • (Human A-F7 TCR ...) x 2
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MAIT cells / MR1 / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...antigen processing and presentation of exogenous antigen / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / MHC class I receptor activity / T cell differentiation in thymus / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
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
XANTHINE / 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: 2.6 Å
AuthorsAwad, W. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Biol.Chem. / Year: 2026
Title: The MHC-I related protein 1 MR1 can bind host purine catabolites.
Authors: Abdelaal, M.R. / Lim, X.Y. / Mak, J.Y.W. / Fairlie, D.P. / McCluskey, J. / Corbett, A.J. / Gherardin, N.A. / Awad, W. / Rossjohn, J.
History
DepositionMay 13, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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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: Human A-F7 TCR TRAV1-2_ALPHA
E: Human A-F7 TCR TRBV6-1_BETA
F: Beta-2-microglobulin
G: Human A-F7 TCR TRAV1-2_ALPHA
H: Human A-F7 TCR TRBV6-1_BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,25221
Polymers188,1008
Non-polymers1,15213
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22900 Å2
ΔGint-125 kcal/mol
Surface area69130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.639, 70.166, 143.705
Angle α, β, γ (deg.)90.000, 104.466, 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 ACBF

#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 / Mutation: C261S
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Human A-F7 TCR ... , 2 types, 4 molecules DGEH

#3: Protein Human A-F7 TCR TRAV1-2_ALPHA


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 Human A-F7 TCR TRBV6-1_BETA


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 , 5 types, 488 molecules

#5: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG3350, BTP, Ca chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953725993633 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725993633 Å / Relative weight: 1
ReflectionResolution: 2.6→46.38 Å / Num. obs: 122238 / % possible obs: 96.88 % / Redundancy: 1.7 % / Biso Wilson estimate: 50.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 1.7
Reflection shellResolution: 2.6→2.63 Å / Num. unique obs: 3902 / CC1/2: 0.586

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.38 Å / SU ML: 0.4042 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2215 3807 3.12 %
Rwork0.1767 118345 -
obs0.1781 122152 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.6 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12643 0 73 475 13191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008313320
X-RAY DIFFRACTIONf_angle_d0.918618191
X-RAY DIFFRACTIONf_chiral_restr0.05121943
X-RAY DIFFRACTIONf_plane_restr0.00762378
X-RAY DIFFRACTIONf_dihedral_angle_d14.79534785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.630.40811200.33913776X-RAY DIFFRACTION84.22
2.63-2.670.32581450.32354432X-RAY DIFFRACTION97.97
2.67-2.70.33221490.29794460X-RAY DIFFRACTION97.81
2.7-2.740.3281370.2864372X-RAY DIFFRACTION97.41
2.74-2.780.34351410.28744451X-RAY DIFFRACTION97.83
2.78-2.830.33691430.2794467X-RAY DIFFRACTION98.17
2.83-2.870.31921420.26264368X-RAY DIFFRACTION97.89
2.87-2.920.33871450.25934494X-RAY DIFFRACTION97.83
2.92-2.980.30151340.25724403X-RAY DIFFRACTION98.08
2.98-3.030.33521400.25114430X-RAY DIFFRACTION97.8
3.03-3.090.33481420.2484423X-RAY DIFFRACTION97.48
3.09-3.160.25541360.2124402X-RAY DIFFRACTION97.84
3.16-3.240.28371400.20854459X-RAY DIFFRACTION97.71
3.24-3.320.24091400.19124361X-RAY DIFFRACTION97.34
3.32-3.410.2411390.18384435X-RAY DIFFRACTION97.55
3.41-3.510.22941470.17184429X-RAY DIFFRACTION97.2
3.51-3.620.23261410.16614263X-RAY DIFFRACTION95.57
3.62-3.750.21231340.16184323X-RAY DIFFRACTION94.81
3.75-3.90.22131450.15364414X-RAY DIFFRACTION96.92
3.9-4.080.1921410.13934417X-RAY DIFFRACTION98.25
4.08-4.290.1661430.12424438X-RAY DIFFRACTION98.62
4.29-4.560.141460.11544479X-RAY DIFFRACTION98.51
4.56-4.910.14511450.11494422X-RAY DIFFRACTION97.98
4.91-5.40.18071450.1334437X-RAY DIFFRACTION97.39
5.4-6.180.19481420.16174313X-RAY DIFFRACTION95.89
6.19-7.790.1931400.17844271X-RAY DIFFRACTION94.45
7.79-46.380.17431450.15574406X-RAY DIFFRACTION97.2
Refinement TLS params.Method: refined / Origin x: 49.809188765504 Å / Origin y: 30.349887974335 Å / Origin z: -49.973725487694 Å
111213212223313233
T0.31877840427561 Å20.045897090567192 Å20.0056421145962001 Å2-0.28879883634658 Å2-0.045164993141965 Å2--0.33145225064214 Å2
L0.25526169405348 °20.02463744425507 °20.10210346607764 °2-0.14086023639166 °2-0.12165994730757 °2--0.37323928436683 °2
S-0.024750520812572 Å °-0.093018584753896 Å °0.045560408897061 Å °0.030287733745153 Å °0.010893649446579 Å °0.010066236064815 Å °-0.018228832498123 Å °-0.094720520991885 Å °0.014406190915822 Å °
Refinement TLS groupSelection details: all

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