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

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Basic information

Entry
Database: PDB / ID: 6bnk
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 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 / positive regulation of macrophage activation ...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 / 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 / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / 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 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AGH / 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: 3.2 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 2.1Jul 7, 2021Group: Structure summary / Category: chem_comp / entity / Item: _chem_comp.pdbx_synonyms / _entity.pdbx_description
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 23, 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)195,88116
Polymers192,4318
Non-polymers3,4508
Water1,838102
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)97,9418
Polymers96,2164
Non-polymers1,7254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-54 kcal/mol
Surface area36400 Å2
MethodPISA
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)97,9418
Polymers96,2164
Non-polymers1,7254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11420 Å2
ΔGint-53 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.970, 150.570, 101.200
Angle α, β, γ (deg.)90.00, 95.23, 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: Escherichia coli (E. coli) / 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: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein NKT Valpha14 (MOUSE) - 2C12 TCR - Hybrid mouse variable and human constant domains


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.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli)

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Sugars , 3 types, 8 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
#7: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C50H99NO9

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Non-polymers , 1 types, 102 molecules

#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 18-20% PEG3350 8% Tacsimate pH 5.0 0.5% dioxane / PH range: 5

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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: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→44.45 Å / Num. obs: 39296 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 57.24 Å2 / Rpim(I) all: 0.102 / Net I/σ(I): 4.8
Reflection shellResolution: 3.2→3.33 Å / Redundancy: 3.4 % / Num. unique obs: 4451 / Rpim(I) all: 0.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QUZ

3quz


Resolution: 3.2→44.45 Å / Cor.coef. Fo:Fc: 0.8891 / Cor.coef. Fo:Fc free: 0.8695 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.382
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 2018 5.14 %RANDOM
Rwork0.2007 ---
obs0.2017 39260 99.69 %-
Displacement parametersBiso mean: 51.11 Å2
Baniso -1Baniso -2Baniso -3
1--3.4401 Å20 Å2-8.251 Å2
2--4.7101 Å20 Å2
3----1.2701 Å2
Refine analyzeLuzzati coordinate error obs: 0.406 Å
Refinement stepCycle: 1 / Resolution: 3.2→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12192 0 232 102 12526
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712770HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917471HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5641SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes281HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1897HARMONIC5
X-RAY DIFFRACTIONt_it12770HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.99
X-RAY DIFFRACTIONt_other_torsion2.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1737SEMIHARMONIC5
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_contact13162SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2814 146 5.04 %
Rwork0.2563 2752 -
all0.2575 2898 -
obs--99.76 %
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)
12.7021-0.29340.67130.9181-0.70391.71790.0239-0.48470.01890.155-0.0678-0.0196-0.1160.10060.0439-0.0971-0.0771-0.051-0.05480.0342-0.108124.863-14.153833.8973
26.8296-0.7922-0.5441.84930.19221.9006-0.0094-0.0004-0.2747-0.23690.0099-0.277-0.03660.5145-0.0005-0.2331-0.0022-0.07660.08250.1445-0.01643.5403-17.297727.7432
32.59010.13312.02521.1817-0.05722.69560.009-0.199-0.1772-0.18820.02720.13780.0922-0.1849-0.0362-0.1078-0.0064-0.0454-0.17880.01460.0956-23.3634-24.2887-3.7581
42.0544-0.96971.65750.7024-0.29611.31470.10650.1652-0.1335-0.1699-0.05690.1385-0.06870.1018-0.0496-0.0017-0.0202-0.0395-0.11510.03920.0157-14.4403-10.4921-14.0166
51.94080.3347-1.68642.01661.53082.57540.2880.008-0.02710.8227-0.27620.18380.3768-0.2797-0.01180.0552-0.13230.1753-0.21660.0367-0.152617.0765-54.988133.6061
610.24680.9281-0.02010.0991-0.337-0.08950.01420.12150.4030.04760.00540.6836-0.0309-0.3717-0.0196-0.40680.10270.25070.1722-0.02410.1241-2.2307-51.851728.8373
72.5797-0.11-2.18231.12480.13083.04670.0336-0.24880.1626-0.1844-0.0335-0.2251-0.110.1991-0.0001-0.0642-0.0057-0.0113-0.2241-0.00050.099463.7481-45.2334-3.8599
82.1894-0.8244-1.4251.04880.22931.85520.04930.2820.1277-0.239-0.0715-0.0281-0.0044-0.23490.02210.0014-0.0034-0.0544-0.1566-0.0411-0.056554.6624-58.7982-14.4769
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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