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- PDB-4apq: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in comp... -

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Basic information

Entry
Database: PDB / ID: 4apq
TitleCrystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide
Components
  • (MOUSE NKT TCR ...) x 2
  • ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
  • BETA-2-MICROGLOBULIN
KeywordsIMMUNE SYSTEM / IMMUNITY / APC CELL SURFACE
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-CIS / T cell receptor alpha chain constant / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsClarke, A.J. / Le Nours, J. / Rossjohn, J.
CitationJournal: To be Published
Title: Type-II Natural Killer T Cell Antigen Receptor Mediated Recognition of Cd1D-Sulfatide
Authors: Patel, O. / Pellicci, D.G. / Gras, S. / Clarke, A.J. / Sandoval-Romero, M. / Le Nours, J. / Theodossis, A. / Mallevaey, T. / Gapin, L. / Cardell, S. / Godfrey, D.I. / Rossjohn, J.
History
DepositionApr 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Derived calculations / Category: struct_conn
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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 2.2Oct 23, 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 TCR VALPHA14, HUMAN NKT TCR VALPHA14
D: MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1188
Polymers96,4684
Non-polymers2,6504
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-23.4 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.110, 95.110, 291.400
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 , 2 types, 2 molecules AB

#1: Protein ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1 / CD1D.1 / CD1D


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P11609
#2: 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) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P01887

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MOUSE NKT TCR ... , 2 types, 2 molecules CD

#3: Protein MOUSE NKT TCR VALPHA14, HUMAN NKT TCR VALPHA14


Mass: 22779.180 Da / Num. of mol.: 1
Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P01848*PLUS
#4: Protein MOUSE NKT TCR AUTOREACTIVE-VBETA6, HUMAN NKT TCR AUTOREACTIVE-VBETA6


Mass: 27366.568 Da / Num. of mol.: 1
Fragment: MOUSE VARIABLE DOMAIN, RESIDUES 1-121, HUMAN CONSTANT DOMAIN, RESIDUES 122-247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): RIL

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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-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 3 molecules

#8: Chemical ChemComp-CIS / (15Z)-N-((1S,2R,3E)-2-HYDROXY-1-{[(3-O-SULFO-BETA-D-GALACTOPYRANOSYL)OXY]METHYL}HEPTADEC-3-ENYL)TETRACOS-15-ENAMIDE / (2S,3R,4E)-N-NERVONIC-1-[BETA-D-(3-SULFATE)-GALACTOPYRANOSYL]-2-AMINO-OCTADECENE-3-OL / CIS-TETRACOSENOYL SULFATIDE


Mass: 890.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H91NO11S
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsBETA-D-MANNOSE (BMA): GLYCOSYLATION FROM EXPRESSION CELL LINE ALPHA-D-MANNOSE (MAN): GLYCOSYLATION ...BETA-D-MANNOSE (BMA): GLYCOSYLATION FROM EXPRESSION CELL LINE ALPHA-D-MANNOSE (MAN): GLYCOSYLATION FROM EXPRESSION CELL LINE N-ACETYL-D-GLUCOSAMINE (NAG): GLYCOSYLATION FROM EXPRESSION CELL LINE

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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: 3.42 Å3/Da / Density % sol: 64.01 % / Description: NONE
Crystal growpH: 6.2 / Details: 0.2M SODIUM CITRATE PH 6.2, 15% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95371
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2012
RadiationMonochromator: DCM VESSEL (DOUBLE CRYSTAL MONOCHROMATOR) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 3→79.6 Å / Num. obs: 27729 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 95.48 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.3 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SCM

3scm


Resolution: 3→36.49 Å / Cor.coef. Fo:Fc: 0.9443 / Cor.coef. Fo:Fc free: 0.9184 / SU R Cruickshank DPI: 1.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.287 / SU Rfree Blow DPI: 0.334 / SU Rfree Cruickshank DPI: 0.337
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 1391 5.03 %RANDOM
Rwork0.1775 ---
obs0.1802 27627 99.56 %-
Displacement parametersBiso mean: 94.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.4059 Å20 Å20 Å2
2--1.4059 Å20 Å2
3----2.8117 Å2
Refine analyzeLuzzati coordinate error obs: 0.491 Å
Refinement stepCycle: LAST / Resolution: 3→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 138 2 6526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016714HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.199170HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3002SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes988HARMONIC5
X-RAY DIFFRACTIONt_it6714HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion3.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion908SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7130SEMIHARMONIC4
LS refinement shellResolution: 3→3.11 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2835 150 5.44 %
Rwork0.226 2609 -
all0.2292 2759 -
obs--99.56 %
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)
12.2341-1.64871.41643.3713-1.92611.97890.36880.16510.0703-0.0772-0.2617-0.2566-0.01720.157-0.1071-0.08080.01320.0256-0.08690.2024-0.09343.9707-116-41.9452
22.2412-1.72391.21543.6517-2.85194.53870.1033-0.37820.07630.67180.1364-0.0552-0.5587-0.4033-0.23970.0783-0.053-0.059-0.04890.2223-0.00842.6963-117.379-24.6073
32.61640.1322-1.21765.2272-0.6712.11980.3809-0.01050.67260.236-0.2956-0.1916-0.31650.5156-0.0853-0.13980.02640.2825-0.24430.21450.0396-8.8031-58.7776-66.4301
43.28910.3816-1.08412.9521-0.62371.20750.3597-0.16420.89450.3472-0.20710.5272-0.30570.0038-0.1526-0.06190.09430.2997-0.28880.16070.0805-26.3119-61.2302-58.2464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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