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- PDB-9eji: Peptide-independent T cell receptor recognition of HLA-DQ2 -

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Basic information

Entry
Database: PDB / ID: 9eji
TitlePeptide-independent T cell receptor recognition of HLA-DQ2
Components
  • (G9 T cell receptor ...) x 2
  • (HLA class II histocompatibility antigen DQ ...) x 2
  • glut-L1 peptide
KeywordsIMMUNE SYSTEM / T cell receptor / immune receptor / human leukocyte antigen
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / HLA class II histocompatibility antigen DQ beta chain / HLA class II histocompatibility antigen DQ alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLim, J.J. / Loh, T.J. / Reid, H.H. / Rossjohn, J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: A naturally selected alpha beta T cell receptor binds HLA-DQ2 molecules without co-contacting the presented peptide.
Authors: Lim, J.J. / Jones, C.M. / Loh, T.J. / Dao, H.T. / Tran, M.T. / Tye-Din, J.A. / La Gruta, N.L. / Rossjohn, J.
History
DepositionNov 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen DQ alpha chain
B: HLA class II histocompatibility antigen DQ beta chain
C: glut-L1 peptide
D: G9 T cell receptor alpha chain
E: G9 T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,35512
Polymers95,3485
Non-polymers1,0077
Water9,440524
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.840, 81.827, 143.167
Angle α, β, γ (deg.)90.000, 107.924, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11D-550-

HOH

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Components

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HLA class II histocompatibility antigen DQ ... , 2 types, 2 molecules AB

#1: Protein HLA class II histocompatibility antigen DQ alpha chain / HLA-DQA1 protein / MHC class II antigen / Major histocompatibility complex / class II / DQ alpha 1


Mass: 20951.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q08AS3
#2: Protein HLA class II histocompatibility antigen DQ beta chain / MHC class II antigen


Mass: 22839.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A0U5IHY9

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide glut-L1 peptide


Mass: 1419.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Baculovirus expression vector pFastBac1-HM

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G9 T cell receptor ... , 2 types, 2 molecules DE

#4: Protein G9 T cell receptor alpha chain


Mass: 22841.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Protein G9 T cell receptor beta chain


Mass: 27296.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Sugars , 2 types, 2 molecules

#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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.: 1 / 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

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Non-polymers , 3 types, 529 molecules

#7: 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% Tacsimate pH 8.0, 20-24% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.2→48.45 Å / Num. obs: 56955 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 27.11 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.7
Reflection shellResolution: 2.2→2.26 Å / Num. unique obs: 4668 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.45 Å / SU ML: 0.2359 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 2955 5.19 %
Rwork0.1852 53957 -
obs0.1871 56912 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 76 524 7042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226676
X-RAY DIFFRACTIONf_angle_d0.56939078
X-RAY DIFFRACTIONf_chiral_restr0.04291004
X-RAY DIFFRACTIONf_plane_restr0.00461183
X-RAY DIFFRACTIONf_dihedral_angle_d5.3095902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.27721220.22092566X-RAY DIFFRACTION99.78
2.24-2.270.30791440.21232572X-RAY DIFFRACTION99.71
2.27-2.320.2561590.21672508X-RAY DIFFRACTION99.93
2.32-2.360.28151340.20882555X-RAY DIFFRACTION99.85
2.36-2.410.24861520.21532546X-RAY DIFFRACTION99.93
2.41-2.460.29981250.20932593X-RAY DIFFRACTION100
2.46-2.520.26571400.21192535X-RAY DIFFRACTION99.93
2.52-2.580.24041400.2082542X-RAY DIFFRACTION100
2.58-2.650.28841420.20582579X-RAY DIFFRACTION99.82
2.65-2.730.25361250.2152581X-RAY DIFFRACTION100
2.73-2.820.2621360.21282580X-RAY DIFFRACTION99.89
2.82-2.920.24951500.20852552X-RAY DIFFRACTION99.93
2.92-3.030.24611560.21712531X-RAY DIFFRACTION99.96
3.03-3.170.24331180.18882597X-RAY DIFFRACTION100
3.17-3.340.19371570.18332525X-RAY DIFFRACTION99.96
3.34-3.550.19531500.17672590X-RAY DIFFRACTION100
3.55-3.820.24351330.17012575X-RAY DIFFRACTION99.96
3.82-4.210.17591500.16312575X-RAY DIFFRACTION100
4.21-4.820.16751460.13982593X-RAY DIFFRACTION100
4.82-6.070.18381390.16182600X-RAY DIFFRACTION100
6.07-48.450.18971370.18812662X-RAY DIFFRACTION99.68

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