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

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Basic information

Entry
Database: PDB / ID: 3sdc
TitleCrystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-globotrihexosylceramide
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-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 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 / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / regulation of immune response / cellular defense response / T cell receptor binding / Neutrophil degranulation / positive regulation of interleukin-2 production / 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 / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / sensory perception of smell / late endosome / Downstream TCR signaling / 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 / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-3GB / 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: 3.1 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
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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 TCR Valpha14 chain
D: NKT TCR autoreactive-Vbeta6 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7698
Polymers96,7374
Non-polymers2,0314
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.350, 94.350, 287.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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


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-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 , 2 types, 38 molecules

#7: Chemical ChemComp-3GB / N-[(2S,3R,4E)-1-{[alpha-D-galactopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranosyl]oxy}-3-hydroxyoctadec-4-en-2-yl]hexacosanamide / Globotrihexosylceramide


Mass: 1164.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H117NO18
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 3.31 Å3/Da / Density % sol: 62.85 % / Mosaicity: 0.62 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 13.5% PEG 6000, 0.1M Sodium citrate, pH 6.1, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→89.657 Å / Num. all: 23961 / Num. obs: 23961 / % possible obs: 98.4 % / Redundancy: 5.6 % / Rsym value: 0.222 / Net I/σ(I): 6.9
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.1-3.2761.1240.82074334510.4471.1241.0281.799.1
3.27-3.475.90.7121.21922632630.2850.7120.652.799.1
3.47-3.715.80.4791.81790230900.1940.4790.436498.9
3.71-45.70.3262.61639028650.1330.3260.2975.598.7
4-4.385.60.2141483026500.0860.210.198.298.7
4.38-4.95.40.1485.61317524210.0610.1480.13410.498.3
4.9-5.665.30.1535.41130421230.0640.1530.1389.997.6
5.66-6.9350.1565.2912818240.0670.1560.149.197.8
6.93-9.85.40.0947.8758114130.0390.0940.08514.495.5
9.8-66.7165.90.0846.750718610.0340.0840.07719.996.1

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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: 3.1→66.72 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.853 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7502 / SU B: 24.791 / SU ML: 0.425 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.504 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2921 1225 5.1 %RANDOM
Rwork0.2402 ---
obs0.2429 23951 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 188.08 Å2 / Biso mean: 62.6847 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å20 Å2
2---0.62 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 3.1→66.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6516 0 137 37 6690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226797
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9339219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.566311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.292151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4381529
X-RAY DIFFRACTIONr_chiral_restr0.080.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215122
X-RAY DIFFRACTIONr_mcbond_it0.4291.54076
X-RAY DIFFRACTIONr_mcangle_it0.80126584
X-RAY DIFFRACTIONr_scbond_it0.75332721
X-RAY DIFFRACTIONr_scangle_it1.384.52635
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 89 -
Rwork0.326 1661 -
all-1750 -
obs--98.65 %

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