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- PDB-6mji: Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex -

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Basic information

Entry
Database: PDB / ID: 6mji
TitleCrystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Beta-chain,Tcell receptor chain,T cell receptor beta constant 2
  • T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
KeywordsIMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell activation / positive regulation of NK T cell differentiation / NK T cell differentiation / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell activation / positive regulation of NK T cell differentiation / NK T cell differentiation / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of macrophage activation / 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 / T cell receptor complex / antigen processing and presentation / positive regulation of interleukin-4 production / alpha-beta T cell activation / regulation of immune response / cellular defense response / T cell receptor binding / Neutrophil degranulation / positive regulation of interleukin-2 production / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / late endosome / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / early endosome / lysosome / endosome membrane / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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 / Immunoglobulin V-Type ...: / : / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-JTD / T cell receptor alpha variable 11 / CD1d1 antigen / T cell receptor beta constant 2 / Tcell receptor chain / Beta-chain / Human nkt tcr alpha chain / 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: 2.3 Å
AuthorsZajonc, D.M. / Bitra, A. / Janssens, J.
CitationJournal: ChemMedChem / Year: 2019
Title: 4"-O-Alkylated alpha-Galactosylceramide Analogues as iNKT-Cell Antigens: Synthetic, Biological, and Structural Studies.
Authors: Janssens, J. / Bitra, A. / Wang, J. / Decruy, T. / Venken, K. / van der Eycken, J. / Elewaut, D. / Zajonc, D.M. / van Calenbergh, S.
History
DepositionSep 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
D: Beta-chain,Tcell receptor chain,T cell receptor beta constant 2
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,42716
Polymers94,3764
Non-polymers3,05112
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-45 kcal/mol
Surface area37770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.216, 191.161, 151.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 4 types, 4 molecules CDAB

#1: Protein T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN / T cell receptor alpha variable 11D / Human nkt tcr beta chain


Mass: 23055.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav11, Trav11d, Traj18, B2M, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J1J9, UniProt: K7N5M3
#2: Protein Beta-chain,Tcell receptor chain,T cell receptor beta constant 2


Mass: 27026.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: TRBC2, TCRBC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A2NTY6, UniProt: A0N8J3, UniProt: A0A5B9
#3: Protein Antigen-presenting glycoprotein CD1d1 / MCG3074 / isoform CRA_a


Mass: 32632.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, mCG_3074 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A0R4J090, UniProt: P11609*PLUS
#4: 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 / Details (production host): dual promotor / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01887

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Sugars , 3 types, 3 molecules

#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.: 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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: 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: 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 , 4 types, 405 molecules

#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical ChemComp-JTD / N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide


Mass: 912.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H105NO9
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 m sodium malonate pH 4.0, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 51194 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.049 / Rrim(I) all: 0.121 / Χ2: 1.628 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.384.70.58550040.7430.2970.6590.54598.4
2.38-2.4850.50550280.8260.2480.5650.59798.7
2.48-2.595.90.40550760.8950.1830.4450.65399.8
2.59-2.7360.3150760.9240.1390.3410.82399.9
2.73-2.95.90.23350830.9490.1050.2561.0599.9
2.9-3.125.80.17351060.9680.0770.191.46199.6
3.12-3.446.30.13151160.980.0570.1432.033100
3.44-3.936.10.10751350.9860.0470.1172.77899.8
3.93-4.956.50.08351980.9930.0350.092.91699.8
4.95-506.10.06853720.9960.0290.0742.59199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRS

4irs


Resolution: 2.3→45.61 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.404 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.203
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2551 5 %RANDOM
Rwork0.1892 ---
obs0.1912 48493 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.5 Å2 / Biso mean: 43.911 Å2 / Biso min: 24.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.07 Å2
Refinement stepCycle: final / Resolution: 2.3→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 204 396 6990
Biso mean--61.65 47.84 -
Num. residues----809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0146799
X-RAY DIFFRACTIONr_bond_other_d0.0010.0185851
X-RAY DIFFRACTIONr_angle_refined_deg0.9581.6929243
X-RAY DIFFRACTIONr_angle_other_deg0.7361.69713779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32222.853347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.736151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4761535
X-RAY DIFFRACTIONr_chiral_restr0.0450.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021274
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 164 -
Rwork0.264 3447 -
all-3611 -
obs--96.76 %

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