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- PDB-6bnl: Crystal structure of TCR-MHC-like molecule -

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Basic information

Entry
Database: PDB / ID: 6bnl
TitleCrystal structure of TCR-MHC-like molecule
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
  • NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
KeywordsIMMUNE SYSTEM / Lipids Cancer
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 / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions ...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 / 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 / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / T cell receptor binding / Neutrophil degranulation / positive regulation of interleukin-2 production / 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 / negative regulation of epithelial cell proliferation / sensory perception of smell / late endosome / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / 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 / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-QWV / CD1d1 antigen / 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: 2.6 Å
AuthorsLe Nours, J. / Rossjohn, J.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Dual Modifications of alpha-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity.
Authors: Chennamadhavuni, D. / Saavedra-Avila, N.A. / Carreno, L.J. / Guberman-Pfeffer, M.J. / Arora, P. / Yongqing, T. / Koay, H.F. / Godfrey, D.I. / Keshipeddy, S. / Richardson, S.K. / Sundararaj, ...Authors: Chennamadhavuni, D. / Saavedra-Avila, N.A. / Carreno, L.J. / Guberman-Pfeffer, M.J. / Arora, P. / Yongqing, T. / Koay, H.F. / Godfrey, D.I. / Keshipeddy, S. / Richardson, S.K. / Sundararaj, S. / Lo, J.H. / Wen, X. / Gascon, J.A. / Yuan, W. / Rossjohn, J. / Le Nours, J. / Porcelli, S.A. / Howell, A.R.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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_seq_id / _atom_site_anisotrop.pdbx_label_asym_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_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 2.1Oct 4, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
D: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
H: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,11416
Polymers192,4318
Non-polymers3,6838
Water3,099172
1
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
D: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0578
Polymers96,2164
Non-polymers1,8414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Antigen-presenting glycoprotein CD1d1
F: Beta-2-microglobulin
G: NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains
H: NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0578
Polymers96,2164
Non-polymers1,8414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.666, 150.318, 100.144
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Antigen-presenting glycoprotein CD1d1 / MCG3074 / isoform CRA_a


Mass: 34662.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, mCG_3074 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A0R4J090, UniProt: P11609*PLUS
#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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains / Human nkt tcr beta chain


Mass: 22779.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli)
#4: Protein NKT Vbeta8.2 (MOUSE) - 2C12 TCR - hybrid mouse variable and human constant domains


Mass: 27113.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 6 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.: 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
#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.: 4
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, 174 molecules

#7: Chemical ChemComp-QWV / N-[(2S,3R)-3-hydroxy-1-{[6-O-(3-phenylpropanoyl)-alpha-D-galactopyranosyl]oxy}octadecan-2-yl]hexacosanamide


Mass: 974.482 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H107NO9
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 18-20% PEG3350 8% tacsimate pH 5.0 0.5% dioxane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→83.01 Å / Num. obs: 71925 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 66.88 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 21.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 10545 / Rpim(I) all: 0.375 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QUZ

3quz


Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.333 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.233
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3633 5.05 %RANDOM
Rwork0.181 ---
obs0.183 71877 99.8 %-
Displacement parametersBiso mean: 62.8 Å2
Baniso -1Baniso -2Baniso -3
1--8.3006 Å20 Å2-8.8768 Å2
2--7.9626 Å20 Å2
3---0.338 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.6→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12164 0 250 172 12586
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112788HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1217476HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5682SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2168HARMONIC5
X-RAY DIFFRACTIONt_it12788HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion2.83
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1712SEMIHARMONIC5
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_contact13436SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2584 296 5.52 %
Rwork0.2174 5063 -
all0.2197 5359 -
obs--99.96 %
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)
11.8008-0.35790.3752.0587-0.54942.7847-0.1057-0.21370.08160.5177-0.0943-0.1981-0.08160.43920.2-0.0955-0.0390.0042-0.19510.0057-0.192323.1359-18.970733.4234
26.874-0.59870.09410.9841-1.32592.6278-0.27860.1777-0.01950.0368-0.2141-0.67320.011.08770.4927-0.29720.0242-0.09760.14340.1367-0.031343.8993-21.619927.9369
31.4008-0.19660.91611.0428-0.06651.69260.1064-0.1172-0.1971-0.34540.01930.22190.0235-0.1733-0.1258-0.0103-0.0133-0.0255-0.19180.02810.0759-22.9829-28.885-3.5566
41.6158-0.72861.39610.8465-0.2931.4390.13350.0779-0.1223-0.2948-0.08060.1668-0.11980.1129-0.05290.04560.03610.029-0.2040.0124-0.0894-14.2608-15.1571-14.0173
52.45340.1779-1.55751.4153-0.4172.40920.041-0.0213-0.02920.43790.06860.31110.0047-0.4336-0.1096-0.0555-0.03990.1371-0.16070.0678-0.166817.1198-59.192534.4325
68.08351.1381-1.20790.0022-0.3976-0.1152-0.09010.82650.55550.00170.38230.8712-0.1684-1.0061-0.2921-0.36170.15910.23010.31280.2749-0.0348-2.2639-55.734629.7721
71.5888-0.1985-1.26681.13920.36952.20540.0844-0.14950.1776-0.24890.0357-0.2147-0.14990.1796-0.1201-0.0486-0.03590.065-0.2244-0.02780.065363.6543-49.8519-4.0473
81.051-0.5901-1.10560.78230.2351.58340.12810.21170.1143-0.1915-0.1055-0.12730.0432-0.1628-0.02260.0033-0.02080.0306-0.1612-0.0278-0.037454.3022-63.242-14.2691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

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