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- PDB-9qwj: Crystal structure of S2c TCR in complex with CD1c -

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Basic information

Entry
Database: PDB / ID: 9qwj
TitleCrystal structure of S2c TCR in complex with CD1c
Components
  • Beta-2-microglobulin,T-cell surface glycoprotein CD1c
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / T cell receptor / TCR / CD1c / lipids
Function / homology
Function and homology information


glycolipid binding / T cell activation involved in immune response / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / regulation of natural killer cell mediated immunity / early endosome lumen / positive regulation of T cell mediated cytotoxicity ...glycolipid binding / T cell activation involved in immune response / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / regulation of natural killer cell mediated immunity / early endosome lumen / positive regulation of T cell mediated cytotoxicity / 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 / amyloid fibril formation / protein homotetramerization / adaptive immune response / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / lysosomal membrane / Neutrophil degranulation / 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-I family domain / 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 ...MHC-I family domain / 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-D-mannopyranose / DECANE / DODECANE / T-cell surface glycoprotein CD1c / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsKaruppiah, V.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Front Immunol / Year: 2025
Title: A CD1c lipid agnostic T cell receptor bispecific engager redirects T cells against CD1c + cells.
Authors: Szoke-Kovacs, R. / Khakoo, S. / Rangel, V.L. / Della Cristina, P. / Pentier, J. / Khanolkar, R. / El-Ajouz, S. / Simmons, R. / Cole, D.K. / Gogolak, P. / Salio, M. / Karuppiah, V.
History
DepositionApr 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-2-microglobulin,T-cell surface glycoprotein CD1c
D: TCR alpha
E: TCR beta
N: Beta-2-microglobulin,T-cell surface glycoprotein CD1c
T: TCR alpha
U: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,19630
Polymers199,4806
Non-polymers3,71624
Water9,206511
1
B: Beta-2-microglobulin,T-cell surface glycoprotein CD1c
D: TCR alpha
E: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,85816
Polymers99,7403
Non-polymers2,11813
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
N: Beta-2-microglobulin,T-cell surface glycoprotein CD1c
T: TCR alpha
U: TCR beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,33814
Polymers99,7403
Non-polymers1,59811
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.373, 122.068, 108.696
Angle α, β, γ (deg.)90.00, 110.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules BNDTEU

#1: Protein Beta-2-microglobulin,T-cell surface glycoprotein CD1c


Mass: 49744.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, CD1C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61769, UniProt: P29017
#2: Protein TCR alpha


Mass: 21936.221 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)
#3: Protein TCR beta


Mass: 28059.158 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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Sugars , 3 types, 10 molecules

#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 6 / 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
#7: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 525 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium cacodylate trihydrate pH 6.4, 0.2 M Calcium chloride dihydrate, 16 % (w/v) PEG 3350 and 3 % (w/v) 1,6-Hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.04→102.43 Å / Num. obs: 87692 / % possible obs: 93.2 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.051 / Rrim(I) all: 0.145 / Net I/σ(I): 10.6
Reflection shellResolution: 2.04→2.3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.205 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4386 / CC1/2: 0.668 / Rpim(I) all: 0.468 / Rrim(I) all: 1.294 / % possible all: 61.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→67.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 11.959 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23503 6481 4.9 %RANDOM
Rwork0.20037 ---
obs0.20209 126417 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20.02 Å2
2--0.51 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.04→67.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12818 0 237 511 13566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01213407
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612061
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.81318182
X-RAY DIFFRACTIONr_angle_other_deg0.6171.75527854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.58451594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.006576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.702102117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21942
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215907
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023257
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7362.7566406
X-RAY DIFFRACTIONr_mcbond_other2.7322.7566406
X-RAY DIFFRACTIONr_mcangle_it4.0294.9327987
X-RAY DIFFRACTIONr_mcangle_other4.0294.9337988
X-RAY DIFFRACTIONr_scbond_it3.6023.1677001
X-RAY DIFFRACTIONr_scbond_other3.6023.1677002
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.525.62510195
X-RAY DIFFRACTIONr_long_range_B_refined9.76131.4514129
X-RAY DIFFRACTIONr_long_range_B_other9.76131.4514130
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 432 -
Rwork0.317 9360 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9274-0.2016-0.34021.02050.74192.2713-0.0055-0.0291-0.01750.14530.0044-0.0535-0.06420.16970.0010.0618-0.0234-0.00370.04280.00350.00715.496827.463631.1647
22.6036-0.332-1.90721.56610.05423.481-0.0034-0.3119-0.20370.27610.0050.12380.07120.1903-0.00160.0939-0.02390.02250.07540.01730.03523.677517.150247.3858
31.32990.26571.18881.07411.07363.0726-0.02330.0548-0.0094-0.1649-0.06010.1907-0.2074-0.16050.08330.10020.03070.00680.06030.00730.0572-15.637214.1203-20.6414
40.28630.06330.22790.63250.8242.6486-0.01140.0166-0.01830.0574-0.07920.09590.1466-0.19560.09050.07230.01520.03480.05-0.00070.0677-16.8852-3.4525-12.695
51.17940.2104-0.19410.8359-0.39562.5457-0.00950.08770.003-0.1265-0.00210.0981-0.1258-0.20350.01160.1120.0169-0.04230.0513-0.00440.02645.15926.474925.4772
62.9920.6696-1.59691.229-0.2273.2051-0.01180.3583-0.2328-0.1501-0.0143-0.16060.0276-0.09330.02610.0780.0221-0.01750.1121-0.03150.050546.490615.83739.5434
70.7236-0.38931.17271.1144-0.84673.0328-0.0889-0.08240.08910.08980.0533-0.1611-0.19890.04020.03560.07920.01380.01520.077-0.0230.052663.7716.737778.4727
80.4726-0.22870.74860.6562-0.33192.22260.0119-0.0455-0.0514-0.03370.0462-0.04350.15590.029-0.05810.1003-0.01640.0310.04610.00680.03567.5389-0.708771.3538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 103
2X-RAY DIFFRACTION2B113 - 388
3X-RAY DIFFRACTION3D3 - 201
4X-RAY DIFFRACTION4E2 - 301
5X-RAY DIFFRACTION5N2 - 103
6X-RAY DIFFRACTION6N117 - 388
7X-RAY DIFFRACTION7T2 - 201
8X-RAY DIFFRACTION8U2 - 245

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