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- PDB-3sdd: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in comp... -

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Basic information

Entry
Database: PDB / ID: 3sdd
TitleCrystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulinBeta-2 microglobulin
  • NKT TCR Valpha14 chain
  • NKT TCR autoreactive-Vbeta6 chain
KeywordsIMMUNE SYSTEM / CD1d / autoimmunity / self-recognition / NKT
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / lipid antigen binding / 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 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 / regulation of membrane depolarization / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / antigen processing and presentation / PD-1 signaling / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / Neutrophil degranulation / cell adhesion molecule binding / T cell receptor binding / response to bacterium / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / late endosome / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / histone binding / T cell receptor signaling pathway / protein refolding / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / lysosome / learning or memory / early endosome / endosome membrane / defense response to Gram-positive bacterium / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / identical protein binding / plasma membrane / cytosol
Similarity search - Function
T-cell receptor alpha chain, constant domain / MHC-I family 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 ...T-cell receptor alpha chain, constant domain / MHC-I family 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-3GD / T cell receptor alpha chain constant / 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 Å
AuthorsClarke, A.J. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2011
Title: Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors
Authors: Pellicci, D.G. / Clarke, A.J. / Patel, O. / Mallevaey, T. / Beddoe, T. / Le Nours, J. / Uldrich, A.P. / McCluskey, J. / Besra, G.S. / Porcelli, S.A. / Gapin, L. / Godfrey, D.I. / Rossjohn, J.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: NKT TCR Valpha14 chain
D: NKT TCR autoreactive-Vbeta6 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5518
Polymers96,7374
Non-polymers1,8134
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.469, 94.469, 291.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1.1, Cd1d1 / Plasmid: pFastBac dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pFastBac dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein NKT TCR Valpha14 chain


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
Source: (gene. exp.) Mus musculus , Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: P01848*PLUS
#4: Protein NKT TCR autoreactive-Vbeta6 chain


Mass: 27635.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus , Homo sapiens / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL

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Sugars , 2 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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 , 2 types, 31 molecules

#7: Chemical ChemComp-3GD / N-[(2S,3R,4E)-1-{[4-O-(beta-D-galactopyranosyl)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]docosanamide


Mass: 946.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C52H99NO13
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE ...1. SEQUENCE CONFLICT IN ENTITY 1 IS BASED ON REFERENCE 3 OF DATABASE P11609 (CD1D1_MOUSE). 2. THE SEQUENCE CONFLICT OF ENTITY 2 IS A NATURAL VARIANT ACCORDING TO DATABASE P01887 (B2MG_MOUSE).

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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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG 6000, 0.1M Sodium citrate, pH 6.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→89.855 Å / Num. all: 30294 / Num. obs: 30294 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.111 / Rsym value: 0.102 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.9-3.067.10.81810.8181100
3.06-3.247.10.4761.60.4761100
3.24-3.4770.2630.261100
3.47-3.7470.1614.80.1611100
3.74-4.16.90.1096.90.1091100
4.1-4.596.80.07890.0781100
4.59-5.296.70.0758.60.0751100
5.29-6.486.40.0739.20.0731100
6.48-9.176.20.04912.40.049199.3
9.17-89.8556.20.0413.60.04198.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→89.85 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.833 / Occupancy max: 1 / Occupancy min: 0 / SU B: 24.611 / SU ML: 0.438 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
RfactorNum. reflection% reflectionSelection details
Rfree0.318 1371 5 %random
Rwork0.258 ---
obs0.261 27300 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 3→89.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6495 0 122 30 6647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026758
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.9499170
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7465810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5824.625307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.661528
X-RAY DIFFRACTIONr_chiral_restr0.0570.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215111
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_it0.2581.54067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46526572
X-RAY DIFFRACTIONr_scbond_it0.18132689
X-RAY DIFFRACTIONr_scangle_it0.3364.52589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 92 -
Rwork0.354 1651 -
obs--99.94 %

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