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- PDB-3ard: Ternary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha... -

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Basic information

Entry
Database: PDB / ID: 3ard
TitleTernary crystal structure of the mouse NKT TCR-CD1d-3'deoxy-alpha-galactosylceramide
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18
  • Vbeta8.2,Vbeta8.2
KeywordsIMMUNE SYSTEM / mouse CD1d / mouse NKT TCR
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 / alpha-beta T cell receptor complex ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 / alpha-beta T cell receptor complex / positive regulation of macrophage activation / positive thymic T cell selection / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation / alpha-beta T cell activation / Generation of second messenger molecules / regulation of immune response / PD-1 signaling / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / 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 / 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 / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / 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 / positive regulation of T cell activation / sensory perception of smell / late endosome / negative regulation of neuron projection development / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / lysosome / early endosome / learning or memory / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
: / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / : / 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-3GH / T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWun, K.S. / Rossjohn, J.
CitationJournal: Immunity / Year: 2011
Title: A molecular basis for the exquisite CD1d-restricted antigen specificity and functional responses of natural killer T cells
Authors: Wun, K.S. / Cameron, G. / Patel, O. / Pang, S.S. / Pellicci, D.G. / Sullivan, L.C. / Keshipeddy, S. / Young, M.H. / Uldrich, A.P. / Thakur, M.S. / Richardson, S.K. / Howell, A.R. / ...Authors: Wun, K.S. / Cameron, G. / Patel, O. / Pang, S.S. / Pellicci, D.G. / Sullivan, L.C. / Keshipeddy, S. / Young, M.H. / Uldrich, A.P. / Thakur, M.S. / Richardson, S.K. / Howell, A.R. / Illarionov, P.A. / Brooks, A.G. / Besra, G.S. / McCluskey, J. / Gapin, L. / Porcelli, S.A. / Godfrey, D.I. / Rossjohn, J.
History
DepositionNov 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Jan 22, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18
D: Vbeta8.2,Vbeta8.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,3688
Polymers96,2684
Non-polymers2,1004
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.991, 86.732, 235.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBacP10PH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBacP10PH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#4: Protein Vbeta8.2,Vbeta8.2


Mass: 27166.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera of mouse variable domain and human constant domain,Chimera of mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS

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Antibody / Sugars , 2 types, 4 molecules C

#3: Antibody NKT Valpha14-Jalpha18,NKT Valpha14-Jalpha18


Mass: 22779.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Chimera of mouse variable domain and human constant domain,Chimera of mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#5: 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.: 3
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-XylpN]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 19 molecules

#6: Chemical ChemComp-3GH / N-{(2S,3R)-1-[(3-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide


Mass: 826.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H99NO7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR ...FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR CHAIN D, RESIDUES 1 TO 117 IS MOUSE VARIABLE DOMAIN AND 118-247 IS HUMAN CONSTANT DOMAIN. THE SWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN PLACE OF ASPARTATE. SEQUENCE IN THIS PDB AGREES WITH THE CITATION.

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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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 400, 0.1 Ammonium acetate, 0.1M Bis Tris, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95453 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2010
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 24812 / Num. obs: 24812 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.169.51.0872.335561100
9.49-508.70.05923.3899199.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE6

3he6


Resolution: 3.01→47.76 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 47.306 / SU ML: 0.38 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27721 1260 5.1 %RANDOM
Rwork0.21343 ---
all0.21671 23641 --
obs0.21671 23528 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å2-0 Å2
2--5.74 Å20 Å2
3----6.39 Å2
Refinement stepCycle: LAST / Resolution: 3.01→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 130 18 6466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216637
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.921.9369074
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9265826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41624.152289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82815902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2471527
X-RAY DIFFRACTIONr_chiral_restr0.0580.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215108
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.1571.54154
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.30626657
X-RAY DIFFRACTIONr_scbond_it0.432483
X-RAY DIFFRACTIONr_scangle_it0.6784.52417
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.007→3.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 91 -
Rwork0.297 1623 -
obs-1714 94.75 %
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)
13.1416-1.7420.81514.5467-0.52695.36610.0277-0.2549-0.05150.02350.0390.1595-0.1592-0.1273-0.06670.20380.0015-0.02460.3415-0.24550.2212-14.3523-46.7936-73.7716
22.69540.52160.11042.3628-2.02829.2826-0.0339-0.09670.4525-0.33830.1201-0.2882-0.20670.6919-0.08620.31020.03820.01730.1982-0.17020.2482-6.4935-45.9294-101.0408
36.2688-0.12623.29053.96293.416312.72470.0663-0.26870.10160.1783-0.26780.27620.1536-0.62610.20150.0648-0.00630.06720.2937-0.16430.2197-3.6634-36.7519-42.511
47.4037-0.4234-0.55836.39471.45136.44540.24970.36050.3976-0.1405-0.1835-0.044-0.37030.049-0.06620.3683-0.01290.02260.1911-0.02920.035718.6419-28.1692-15.8765
59.55040.85142.87794.77132.51688.51850.6980.1789-0.94820.094-0.0794-0.14070.94120.2865-0.61870.25240.1258-0.11450.2809-0.1650.287812.8886-51.4302-49.0712
63.5046-0.5522-2.64983.81872.47568.36440.20520.295-0.40920.1849-0.0966-0.33640.35030.2315-0.10860.17260.126-0.15690.2332-0.09340.321324.1207-43.5665-21.2047
73.6718-0.0930.24463.48121.61235.3479-0.2689-0.05080.4288-0.43980.2780.08820.0372-0.0375-0.00910.31180.0593-0.05950.19750.11080.1544-23.3568-50.6714-112.0269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 185
2X-RAY DIFFRACTION1A304 - 305
3X-RAY DIFFRACTION1A400 - 401
4X-RAY DIFFRACTION1A501 - 502
5X-RAY DIFFRACTION1A307
6X-RAY DIFFRACTION2B1 - 99
7X-RAY DIFFRACTION3C1 - 112
8X-RAY DIFFRACTION4C113 - 204
9X-RAY DIFFRACTION5D3 - 117
10X-RAY DIFFRACTION6D118 - 246
11X-RAY DIFFRACTION7A186 - 300

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