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- PDB-3tn0: Structure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylcera... -

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Basic information

Entry
Database: PDB / ID: 3tn0
TitleStructure of mouse Va14Vb8.2NKT TCR-mouse CD1d-a-C-Galactosylceramide complex
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2 microglobulin
  • mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
  • mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
KeywordsIMMUNE SYSTEM / mouse CD1d / mouse NKT
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-QUX / T cell receptor alpha chain constant / T cell receptor beta constant 1 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2011
Title: NKT TCR Recognition of CD1d-{alpha}-C-Galactosylceramide.
Authors: Patel, O. / Cameron, G. / Pellicci, D.G. / Liu, Z. / Byun, H.S. / Beddoe, T. / McCluskey, J. / Franck, R.W. / Castano, A.R. / Harrak, Y. / Llebaria, A. / Bittman, R. / Porcelli, S.A. / ...Authors: Patel, O. / Cameron, G. / Pellicci, D.G. / Liu, Z. / Byun, H.S. / Beddoe, T. / McCluskey, J. / Franck, R.W. / Castano, A.R. / Harrak, Y. / Llebaria, A. / Bittman, R. / Porcelli, S.A. / Godfrey, D.I. / Rossjohn, J.
History
DepositionSep 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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 / 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.occupancy / _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.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 / _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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
D: mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9928
Polymers96,2684
Non-polymers1,7234
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.171, 86.368, 236.403
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: UNP residues 19-297
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 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, RP23-34E24.5-001, mCG_11606 / Plasmid: pBacp10pH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS
#4: Protein mouse NKT Vbeta8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)


Mass: 27166.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN D, RESIDUES 1 TO 117 IS MOUSE VARIABLE DOMAIN AND 118-247 IS HUMAN CONSTANT DOMAIN
Source: (gene. exp.) HOMO SAPIENS, Mus musculus / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS

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Antibody / Non-polymers , 2 types, 2 molecules C

#3: Antibody mouse NKT Valpha14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)


Mass: 22779.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN
Source: (gene. exp.) HOMO SAPIENS, Mus musculus / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#6: Chemical ChemComp-QUX / N-[(3S,4S,5R)-4,5-dihydroxy-1-[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]nonadecan-3-yl]hexacosanamide


Mass: 856.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H101NO8

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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
#7: 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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Details

Has protein modificationY
Sequence detailsSWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN PLACE OF ...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: 2

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15-17% PEG 10K, 0.1M ammonium acetat, 0.1M BisTris pH 5.5, 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 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95453 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 20725 / Num. obs: 20725 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.272 / Net I/σ(I): 7.2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2959 / % possible all: 100

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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: PDB entry 3HE6

3he6


Resolution: 3.2→48.77 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.848 / SU B: 63.025 / SU ML: 0.473 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2887 1056 5.1 %
Rwork0.22537 --
all0.2286 19755 -
obs0.2286 19666 99.55 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.224 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å2-0 Å2
2--7.32 Å20 Å2
3----7.95 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6471 0 116 0 6587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216776
X-RAY DIFFRACTIONr_angle_refined_deg1.0051.9399236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375823
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73724.281313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.564151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3661532
X-RAY DIFFRACTIONr_chiral_restr0.0650.21010
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215210
X-RAY DIFFRACTIONr_mcbond_it0.1771.54137
X-RAY DIFFRACTIONr_mcangle_it0.34426673
X-RAY DIFFRACTIONr_scbond_it0.44232639
X-RAY DIFFRACTIONr_scangle_it0.7614.52563
LS refinement shellResolution: 3.2→3.284 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 57 -
Rwork0.335 1360 -
obs-1417 94.15 %
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)
12.00970.49841.3113.53270.0285.28890.08510.440.0206-0.0709-0.1237-0.21940.0090.47050.03850.22630.0356-0.03460.44390.15180.288914.8633-47.350973.9446
24.58030.8507-0.95854.1046-2.20773.7925-0.2828-0.16330.51160.51590.1177-0.1257-0.03460.03130.16510.482-0.0221-0.09120.1483-0.13760.202823.1904-50.3904112.4135
34.8994-0.19620.56823.83254.283911.0721-0.09560.04070.45010.4870.14380.2442-0.1267-0.8361-0.04810.36550.09770.08380.21090.16610.29376.0592-45.925101.1338
44.5428-1.05357.12413.6906-2.897615.69620.2640.74150.3685-0.1177-0.1163-0.18170.09141.0081-0.14770.05090.00480.08190.56770.20640.29453.8415-37.109941.6244
511.5038-0.5652-2.67857.8605-0.61889.80910.0889-0.41310.48440.5835-0.1181-0.0301-0.41760.04880.02920.4252-0.0066-0.03750.10010.02460.0487-18.3431-27.837715.8183
610.1952-1.07912.90456.3189-3.29586.17780.75750.0595-0.924-0.5661-0.08080.09911.0907-0.2987-0.67670.3756-0.0245-0.08460.31660.13220.3107-13.0422-52.128548.8918
74.97490.8507-4.18924.1064-2.561910.16310.2372-0.4522-0.5235-0.3189-0.02320.20480.4331-0.6302-0.21410.1867-0.076-0.17260.220.13640.43-23.8334-43.886620.938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 186
2X-RAY DIFFRACTION1A1
3X-RAY DIFFRACTION1A303
4X-RAY DIFFRACTION1A304
5X-RAY DIFFRACTION1A305 - 306
6X-RAY DIFFRACTION2A187 - 299
7X-RAY DIFFRACTION3B2 - 99
8X-RAY DIFFRACTION4C4 - 116
9X-RAY DIFFRACTION5C117 - 208
10X-RAY DIFFRACTION6D5 - 117
11X-RAY DIFFRACTION7D118 - 246

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