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- PDB-2q7y: Structure of the endogenous iNKT cell ligand iGb3 bound to mCD1d -

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Basic information

Entry
Database: PDB / ID: 2q7y
TitleStructure of the endogenous iNKT cell ligand iGb3 bound to mCD1d
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1d1
KeywordsIMMUNE SYSTEM / antigen presenting molecule / MHC fold / NKT cells
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 / positive thymic T cell selection ...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 / 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 / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...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-IGC / PALMITIC ACID / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZajonc, D.M. / Wilson, I.A. / Teyton, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structures of Mouse CD1d-iGb3 Complex and its Cognate Valpha14 T Cell Receptor Suggest a Model for Dual Recognition of Foreign and Self Glycolipids.
Authors: Zajonc, D.M. / Savage, P.B. / Bendelac, A. / Wilson, I.A. / Teyton, L.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _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.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_seq_id / _struct_conn.ptnr1_label_asym_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,34614
Polymers88,5864
Non-polymers4,76010
Water6,323351
1
A: T-cell surface glycoprotein CD1d1
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0187
Polymers44,2932
Non-polymers2,7255
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint6.4 kcal/mol
Surface area19200 Å2
MethodPISA
2
C: T-cell surface glycoprotein CD1d1
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3287
Polymers44,2932
Non-polymers2,0355
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-7.8 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.941, 96.224, 77.926
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiologically active unit is a heterodimer of mCD1d and beta2M

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein T-cell surface glycoprotein CD1d1 / CD1.1 antigen


Mass: 32632.668 Da / Num. of mol.: 2 / Fragment: residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P11609
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01887

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 3
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, 355 molecules

#6: Chemical ChemComp-IGC / N-[(1S,2R,3E)-1-({[ALPHA-D-GALACTOPYRANOSYL-(1->3)-BETA-D-GALACTOPYRANOSYL-(1->4)-BETA-D-GLUCOPYRANOSYL]OXY}METHYL)-2-H YDROXYHEPTADEC-3-EN-1-YL]OCTANAMIDE / ISOGLOBOTRIHEXOSYLCERAMIDE


Mass: 912.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H81NO18
#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 18% PEG 4000, 0.2 M ammonium citrate, 2% butanol, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2006
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 61120 / Num. obs: 59816 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 26 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.32 / Num. unique all: 5934 / Rsym value: 0.449 / % possible all: 97.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AKR

2akr


Resolution: 1.95→27.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.582 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1219 2.1 %RANDOM
Rwork0.199 ---
all0.2 59295 --
obs0.2 58076 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.361 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.03 Å2
2---0.04 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 288 351 6589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226434
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9798736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9855728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00824.178292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.811151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0471530
X-RAY DIFFRACTIONr_chiral_restr0.1230.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024786
X-RAY DIFFRACTIONr_nbd_refined0.2090.22542
X-RAY DIFFRACTIONr_nbtor_refined0.310.24218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.217
X-RAY DIFFRACTIONr_mcbond_it0.9971.53801
X-RAY DIFFRACTIONr_mcangle_it1.47825954
X-RAY DIFFRACTIONr_scbond_it2.30133097
X-RAY DIFFRACTIONr_scangle_it3.3774.52782
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 91 -
Rwork0.234 4244 -
obs-4335 97.31 %
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)
12.5640.18511.40951.10120.17983.81910.0086-0.0722-0.0177-0.0067-0.00510.13350.0678-0.2907-0.0035-0.1396-0.010.0371-0.12260.0248-0.1156-9.442911.64566.6486
24.72981.8625-0.15997.2504-1.07991.6851-0.04280.27320.507-0.3935-0.1214-0.5076-0.14010.28070.1643-0.0524-0.0365-0.0015-0.1040.0515-0.022921.972234.29759.9715
36.1950.22822.77292.1060.21733.51190.01940.1693-0.338-0.07370.0472-0.26080.02640.2799-0.0666-0.14120.01510.0393-0.11860.011-0.105519.765112.30729.1504
42.08980.09081.20020.77560.18623.70580.0061-0.0075-0.0388-0.00230.00470.13170.1383-0.1711-0.0108-0.1578-0.00420.0362-0.1490.0169-0.13448.854911.078743.3332
52.80851.09510.09734.9903-0.0231.4248-0.06780.22940.2257-0.4034-0.0179-0.5119-0.16050.21120.0858-0.0935-0.00780.0238-0.12910.0253-0.097939.704433.503449.6938
66.34250.05972.58741.36990.32973.30280.04440.2612-0.3399-0.0670.0452-0.18070.03390.2694-0.0895-0.13690.01150.0453-0.147-0.0086-0.154937.695211.716845.9326
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1857 - 185
2X-RAY DIFFRACTION1AF - G501 - 5151 - 5
3X-RAY DIFFRACTION1AK6011
4X-RAY DIFFRACTION1AM7011
5X-RAY DIFFRACTION2AA186 - 279186 - 279
6X-RAY DIFFRACTION3BB2 - 992 - 99
7X-RAY DIFFRACTION4CC7 - 1857 - 185
8X-RAY DIFFRACTION4CH - J500 - 5031 - 2
9X-RAY DIFFRACTION4CL6021
10X-RAY DIFFRACTION4CN7021
11X-RAY DIFFRACTION5CC186 - 279186 - 279
12X-RAY DIFFRACTION6DD2 - 992 - 99

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