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- PDB-3vwj: Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex -

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Basic information

Entry
Database: PDB / ID: 3vwj
TitleTernary crystal structure of the human NKT TCR-CD1d-C20:2 complex
Components
  • (NKT15 T cell receptor ...) x 2
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / CD1D / NKT T CELL RECEPTOR / ALPHA-GALACTOSYLCERAMIDE / PROTEIN RECEPTOR COMPLEX / CELL MEMBRANE / DISULFIDE BOND / ENDOSOME / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / INNATE IMMUNITY / LYSOSOME / MEMBRANE / TRANSMEMBRANE / DISEASE MUTATION / GLYCATION / MHC I / PYRROLIDONE CARBOXYLIC ACID / SECRETED
Function / homology
Function and homology information


lipid antigen binding / T cell selection / 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 / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / T cell selection / 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 / positive regulation of innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 ...MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DB3 / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.093 Å
AuthorsWun, K.S. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Human and mouse type I natural killer T cell antigen receptors exhibit different fine specificities for CD1d-antigen complex
Authors: Wun, K.S. / Ross, F. / Patel, O. / Besra, G.S. / Porcelli, S.A. / Richardson, S.K. / Keshipeddy, S. / Howell, A.R. / Godfrey, D.I. / Rossjohn, J.
History
DepositionAug 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Structure summary
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: NKT15 T cell receptor alpha-chain
D: NKT15 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5708
Polymers95,3334
Non-polymers1,2374
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-3 kcal/mol
Surface area17660 Å2
Unit cell
Length a, b, c (Å)145.930, 176.910, 82.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11D-301-

MG

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 32324.383 Da / Num. of mol.: 1 / Fragment: UNP residues 21-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac Dual / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P15813
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pFastBac Dual / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P61769

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NKT15 T cell receptor ... , 2 types, 2 molecules CD

#3: Protein NKT15 T cell receptor alpha-chain


Mass: 23227.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein NKT15 T cell receptor beta-chain


Mass: 28033.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 1 types, 2 molecules

#5: 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.: 2
Source method: isolated from a genetically manipulated source
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, 19 molecules

#6: Chemical ChemComp-DB3 / (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide


Mass: 770.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H83NO9
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 56.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 8% PEG 10000, 0.2M magnesium chloride, 0.1M Tris, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.093→100 Å / Num. obs: 19938 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12 % / Biso Wilson estimate: 85 Å2 / Net I/σ(I): 4.8
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3.1-3.2712.22.128541100
9.8-10010.76.8703199.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HUJ

3huj


Resolution: 3.093→72.965 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.48 / σ(F): 0 / σ(I): 0 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2922 1011 5.07 %RANDOM
Rwork0.228 ---
all0.2312 19924 --
obs0.2312 19924 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 180.75 Å2 / Biso mean: 69.2126 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: LAST / Resolution: 3.093→72.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5869 0 83 17 5969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036119
X-RAY DIFFRACTIONf_angle_d0.7148358
X-RAY DIFFRACTIONf_dihedral_angle_d12.7952051
X-RAY DIFFRACTIONf_chiral_restr0.047949
X-RAY DIFFRACTIONf_plane_restr0.0031061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.093-3.25610.36711540.2963254896
3.2561-3.46010.36261460.26692684100
3.4601-3.72720.30431330.24552702100
3.7272-4.10230.2851550.23092677100
4.1023-4.69580.27591350.19862716100
4.6958-5.91580.29291480.20672738100
5.9158-72.98530.24821400.22472848100
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)
12.72540.3179-0.09561.2552-0.16934.54040.29380.2381-0.2559-0.29680.01030.05420.9370.3251-0.20090.6560.19-0.20220.38020.01340.3866-18.560727.722-4.6836
25.1884-1.0613-1.55594.56010.77484.9021-0.1973-0.752-0.6668-1.27570.04611.70890.997-0.0586-0.12121.1329-0.1162-0.22530.55990.22610.8322-20.550110.481927.3078
35.3114-2.17492.08884.7675-0.41377.03320.0175-0.25780.21290.16960.1021-0.3436-0.20930.1883-0.12220.4965-0.0724-0.11570.35310.15090.3438-12.24528.75122.9314
44.9727-0.2771-4.81820.82580.64797.2909-0.09260.368-0.173-0.0260.0658-0.0140.2772-0.01410.00850.42080.0566-0.01850.3637-0.01320.2652-11.240944.6534-34.2149
52.92650.814-0.43124.53671.92392.64750.1310.7680.5692-0.75110.0285-0.5416-0.6201-0.0073-0.13010.65040.03480.16230.65740.27550.7161-6.12270.803-56.7052
64.95442.8427-2.82768.2873-3.65985.75030.40340.76870.50680.0142-0.01890.2104-0.5369-0.0788-0.40460.54560.230.12320.62960.0820.349-25.116759.0237-23.5066
72.1332-0.3065-0.76222.0731.5291.27830.42760.3350.277-0.62280.17340.591-0.718-0.33-0.50690.9960.15310.04691.14740.53210.7625-22.417474.9757-49.8565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 8:181)A8 - 181
2X-RAY DIFFRACTION2(chain A and resid 182:278)A182 - 278
3X-RAY DIFFRACTION3(chain B and resid 1:97)B1 - 97
4X-RAY DIFFRACTION4(chain C and resid 1:114)C1 - 114
5X-RAY DIFFRACTION5(chain C and resid 115:206)C115 - 206
6X-RAY DIFFRACTION6(chain D and resid 3:120)D3 - 120
7X-RAY DIFFRACTION7(chain D and resid 121:246)D121 - 246

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