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- PDB-8xub: Crystal structure of Y-50 TCR -

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Basic information

Entry
Database: PDB / ID: 8xub
TitleCrystal structure of Y-50 TCR
Components
  • Y-50 alpha
  • Y-50 beta
KeywordsIMMUNE SYSTEM / TCR complex
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAsa, M. / Nagae, M. / Yamasaki, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H00403 Japan
Japan Society for the Promotion of Science (JSPS)22A304 Japan
CitationJournal: J Clin Invest / Year: 2024
Title: A conserved human CD4+ T cell subset recognizing the mycobacterial adjuvant trehalose monomycolate.
Authors: Yuki Sakai / Minori Asa / Mika Hirose / Wakana Kusuhara / Nagatoshi Fujiwara / Hiroto Tamashima / Takahiro Ikazaki / Shiori Oka / Kota Kuraba / Kentaro Tanaka / Takashi Yoshiyama / Masamichi ...Authors: Yuki Sakai / Minori Asa / Mika Hirose / Wakana Kusuhara / Nagatoshi Fujiwara / Hiroto Tamashima / Takahiro Ikazaki / Shiori Oka / Kota Kuraba / Kentaro Tanaka / Takashi Yoshiyama / Masamichi Nagae / Yoshihiko Hoshino / Daisuke Motooka / Ildiko Van Rhijn / Xiuyuan Lu / Eri Ishikawa / D Branch Moody / Takayuki Kato / Shinsuke Inuki / Go Hirai / Sho Yamasaki /
Abstract: Mycobacterium tuberculosis causes human tuberculosis (TB). As mycobacteria are protected by a thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most ...Mycobacterium tuberculosis causes human tuberculosis (TB). As mycobacteria are protected by a thick lipid cell wall, humans have developed immune responses against diverse mycobacterial lipids. Most of these immunostimulatory lipids are known as adjuvants acting through innate immune receptors, such as C-type lectin receptors. Although a few mycobacterial lipid antigens activate unconventional T cells, the antigenicity of most adjuvantic lipids is unknown. Here, we identified that trehalose monomycolate (TMM), an abundant mycobacterial adjuvant, activated human T cells bearing a unique αβ T cell receptor (αβTCR). This recognition was restricted by CD1b, a monomorphic antigen-presenting molecule conserved in primates but not mice. Single-cell TCR-RNA-Seq using newly established CD1b-TMM tetramers revealed that TMM-specific T cells were present as CD4+ effector memory T cells in the periphery of uninfected donors but expressed IFN-γ, TNF, and anti-mycobacterial effectors upon TMM stimulation. TMM-specific T cells were detected in cord blood and PBMCs of donors without bacillus Calmette-Guérin vaccination but were expanded in patients with active TB. A cryo-electron microscopy study of CD1b-TMM-TCR complexes revealed unique antigen recognition by conserved features of TCRs, positively charged CDR3α, and long CDR3β regions. These results indicate that humans have a commonly shared and preformed CD4+ T cell subset recognizing a typical mycobacterial adjuvant as an antigen. Furthermore, the dual role of TMM justifies reconsideration of the mechanism of action of adjuvants.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 26, 2025Group: 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: Y-50 alpha
B: Y-50 beta
C: Y-50 alpha
D: Y-50 beta
E: Y-50 alpha
F: Y-50 beta
G: Y-50 alpha
H: Y-50 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,68422
Polymers205,3388
Non-polymers2,34614
Water61334
1
A: Y-50 alpha
B: Y-50 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9696
Polymers51,3342
Non-polymers6354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-45 kcal/mol
Surface area21410 Å2
MethodPISA
2
C: Y-50 alpha
D: Y-50 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7485
Polymers51,3342
Non-polymers4133
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-53 kcal/mol
Surface area21040 Å2
MethodPISA
3
E: Y-50 alpha
F: Y-50 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0946
Polymers51,3342
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-33 kcal/mol
Surface area21070 Å2
MethodPISA
4
G: Y-50 alpha
H: Y-50 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8735
Polymers51,3342
Non-polymers5383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-36 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.113, 168.692, 173.116
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-402-

HOH

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Components

#1: Protein
Y-50 alpha


Mass: 23142.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Protein
Y-50 beta


Mass: 28191.834 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium sulfate, 0.1M Bis-TrispH5.5, 25%PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→47.63 Å / Num. obs: 69976 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 60.27 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.05 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4444 / CC1/2: 0.646 / Rpim(I) all: 0.765

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.03 Å / SU ML: 0.4256 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.2778
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2994 3386 4.84 %
Rwork0.2257 66503 -
obs0.2293 69889 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14195 0 142 34 14371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008914681
X-RAY DIFFRACTIONf_angle_d1.062319908
X-RAY DIFFRACTIONf_chiral_restr0.05782148
X-RAY DIFFRACTIONf_plane_restr0.00932589
X-RAY DIFFRACTIONf_dihedral_angle_d6.68391969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.4761370.34262747X-RAY DIFFRACTION100
2.54-2.570.36621400.33272696X-RAY DIFFRACTION100
2.57-2.610.37831490.31022753X-RAY DIFFRACTION99.97
2.61-2.660.39911390.30812724X-RAY DIFFRACTION99.97
2.66-2.70.39491470.29782717X-RAY DIFFRACTION100
2.7-2.750.39091480.28282738X-RAY DIFFRACTION99.93
2.75-2.80.32891500.2752714X-RAY DIFFRACTION99.93
2.8-2.860.33321240.29022769X-RAY DIFFRACTION100
2.86-2.920.40811420.30872732X-RAY DIFFRACTION100
2.92-2.990.40321500.29752753X-RAY DIFFRACTION100
2.99-3.070.38891200.28632753X-RAY DIFFRACTION100
3.07-3.150.32521440.2642753X-RAY DIFFRACTION100
3.15-3.240.31911330.24642779X-RAY DIFFRACTION100
3.24-3.350.36181240.25242746X-RAY DIFFRACTION100
3.35-3.470.29581600.25122743X-RAY DIFFRACTION100
3.47-3.610.30131300.25122790X-RAY DIFFRACTION100
3.61-3.770.35041300.22942775X-RAY DIFFRACTION99.97
3.77-3.970.27911590.22132761X-RAY DIFFRACTION100
3.97-4.220.29231290.20182792X-RAY DIFFRACTION100
4.22-4.540.25971440.17672812X-RAY DIFFRACTION100
4.54-50.21971740.16262749X-RAY DIFFRACTION100
5-5.720.21851110.18562858X-RAY DIFFRACTION100
5.72-7.20.31511510.21722856X-RAY DIFFRACTION100
7.2-44.030.27071510.19952993X-RAY DIFFRACTION99.4

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