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- PDB-8y6x: Crystal structure of ternary complex of human MR1, ligand #4, and... -

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Basic information

Entry
Database: PDB / ID: 8y6x
TitleCrystal structure of ternary complex of human MR1, ligand #4, and MAIT-TCR A-F7
Components
  • Beta-2-microglobulin
  • MAIT T cell receptor (A-F7) alpha chain
  • MAIT T cell receptor (A-F7) beta chain
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM
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 / innate immune response / lysosomal membrane / 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 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
: / 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: 3.4 Å
AuthorsNagae, M. / Inuki, S. / Yamasaki, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H05183 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Development of Ribityllumazine Analogue as Mucosal-Associated Invariant T Cell Ligands.
Authors: Takasaki, R. / Ito, E. / Nagae, M. / Takahashi, Y. / Matsuoka, T. / Yasue, W. / Arichi, N. / Ohno, H. / Yamasaki, S. / Inuki, S.
History
DepositionFeb 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
D: MAIT T cell receptor (A-F7) alpha chain
E: MAIT T cell receptor (A-F7) beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1605
Polymers93,7884
Non-polymers3721
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-41 kcal/mol
Surface area37400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.494, 125.494, 115.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#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.: 1 / 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.: 1
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
#3: Protein MAIT T cell receptor (A-F7) alpha chain


Mass: 22650.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Protein MAIT T cell receptor (A-F7) beta chain


Mass: 27546.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-A1LXU / 5-(2-oxidanylidenepropyl)-8-[(2~{S},3~{S},4~{R})-2,3,4,5-tetrakis(oxidanyl)pentyl]-1,7-dihydropteridine-2,4,6-trione


Mass: 372.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N4O8 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY
Nonpolymer detailsThe carbonyl group of the ligand A1LXU becomes an imine when forming the Schiff base with Lys.

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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: 4.85 Å3/Da / Density % sol: 74.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1M Tris (pH 8.2), 20mM Magnesium chloride, 22% (v/v) polyacrylic acid sodium salt 5,100

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2023
RadiationMonochromator: Si(1 1 1) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.4→40.3 Å / Num. obs: 24734 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 79.66 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.091 / Net I/σ(I): 9.7
Reflection shellResolution: 3.4→3.52 Å / Num. unique obs: 2439 / CC1/2: 0.58 / Rpim(I) all: 0.508

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→40.25 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 1239 5.01 %
Rwork0.1763 --
obs0.1779 24725 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→40.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6487 0 0 0 6487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036661
X-RAY DIFFRACTIONf_angle_d0.5539041
X-RAY DIFFRACTIONf_dihedral_angle_d4.912878
X-RAY DIFFRACTIONf_chiral_restr0.041950
X-RAY DIFFRACTIONf_plane_restr0.0041170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.540.31481480.26652575X-RAY DIFFRACTION100
3.54-3.70.25261670.22712568X-RAY DIFFRACTION100
3.7-3.890.25551330.22252606X-RAY DIFFRACTION100
3.89-4.140.22611110.18662613X-RAY DIFFRACTION100
4.14-4.450.20531680.15132587X-RAY DIFFRACTION100
4.45-4.90.17951610.14632567X-RAY DIFFRACTION100
4.9-5.610.16031040.15432644X-RAY DIFFRACTION100
5.61-7.060.24291210.18252654X-RAY DIFFRACTION100
7.06-40.250.15831260.15352672X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -72.3157 Å / Origin y: -21.3961 Å / Origin z: -24.7971 Å
111213212223313233
T0.505 Å2-0.0319 Å20.1007 Å2-0.3668 Å20.0315 Å2--0.5835 Å2
L1.3598 °20.3717 °20.9103 °2-0.9323 °20.6084 °2--1.9135 °2
S-0.0203 Å °-0.0012 Å °-0.0007 Å °0.0528 Å °0.027 Å °0.0821 Å °0.2398 Å °-0.131 Å °-0.019 Å °
Refinement TLS groupSelection details: all

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