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- PDB-4mng: Structure of the DP10.7 TCR with CD1d-sulfatide -

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Basic information

Entry
Database: PDB / ID: 4mng
TitleStructure of the DP10.7 TCR with CD1d-sulfatide
Components
  • Beta-2-microglobulin
  • Cd1d1 protein
  • TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
KeywordsIMMUNE SYSTEM / Immunglobulin / Histocompatibility Antigens / CD1 / Immunological / lymphocytes / gamma delta T cell / T cell recognition / self-recognition / myelin / intestinal epithelial lymphocytes / Human / Lipid binding / self-ligand / Glycoproteins / Cell-surface receptors
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / Endosomal/Vacuolar pathway / DAP12 interactions ...lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive regulation of innate immune response / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / heterotypic cell-cell adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / beta-2-microglobulin binding / cellular defense response / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / 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 / 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 / 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 / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / external side of plasma membrane / lysosomal membrane / innate immune response / endoplasmic reticulum membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol / cytoplasm
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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain ...: / MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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 / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d / TRA@ protein / Cd1d1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0058 Å
AuthorsLuoma, A.M. / Adams, E.J.
CitationJournal: Immunity / Year: 2013
Title: Crystal Structure of V delta 1 T Cell Receptor in Complex with CD1d-Sulfatide Shows MHC-like Recognition of a Self-Lipid by Human gamma delta T Cells.
Authors: Luoma, A.M. / Castro, C.D. / Mayassi, T. / Bembinster, L.A. / Bai, L. / Picard, D. / Anderson, B. / Scharf, L. / Kung, J.E. / Sibener, L.V. / Savage, P.B. / Jabri, B. / Bendelac, A. / Adams, E.J.
History
DepositionSep 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Beta-2-microglobulin
A: Cd1d1 protein
D: Beta-2-microglobulin
C: Cd1d1 protein
E: TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
F: TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,44414
Polymers144,3366
Non-polymers3,1088
Water32418
1
B: Beta-2-microglobulin
A: Cd1d1 protein
E: TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7227
Polymers72,1683
Non-polymers1,5544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-24 kcal/mol
Surface area28970 Å2
MethodPISA
2
D: Beta-2-microglobulin
C: Cd1d1 protein
F: TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7227
Polymers72,1683
Non-polymers1,5544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-24 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.333, 229.333, 52.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 2 types, 4 molecules BDAC

#1: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2 / Fragment: Beta-2-microglobulin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pACgp67a / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P01887
#2: Protein Cd1d1 protein


Mass: 31972.771 Da / Num. of mol.: 2 / Fragment: CD1d,CD1d
Mutation: human CD1d alpha3 domain replaced with mouse CD1d alpha3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pACgp67a / Gene: Cd1d1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five / References: UniProt: P15813, UniProt: Q7TMK5

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Antibody / Sugars , 2 types, 8 molecules EF

#3: Antibody TRA@ protein,TRA@ protein, Ti antigen CD3-associated protein gamma chain V-J-C region


Mass: 28534.943 Da / Num. of mol.: 2
Fragment: Single chain of delta and gamma variable domains,Single chain of delta and gamma variable domains
Mutation: end of gamma sequence TLVV swapped with KLII
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3 / References: UniProt: Q6PJ56
#4: 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.: 6
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, 20 molecules

#5: 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.: 2 / Source method: obtained synthetically / Formula: C48H91NO11S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 5.54 Å3/Da / Density % sol: 77.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 11% PEG 4000 5% isopropanol 2 mM glutathione reduced/oxidized 50 mM tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 24, 2013
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 61100 / Num. obs: 61100 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 %
Reflection shellResolution: 3→3.05 Å / % possible all: 95.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4MNH and 4MQ7

4mnh

4mq7


Resolution: 3.0058→49.652 Å / SU ML: 0.35 / σ(F): 1.97 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 3091 5.06 %
Rwork0.1779 --
obs0.1794 61056 98.99 %
all-61058 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.0058→49.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9551 0 206 18 9775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310041
X-RAY DIFFRACTIONf_angle_d0.79513625
X-RAY DIFFRACTIONf_dihedral_angle_d11.8243617
X-RAY DIFFRACTIONf_chiral_restr0.0571475
X-RAY DIFFRACTIONf_plane_restr0.0061709
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0058-3.05280.30491340.28112548X-RAY DIFFRACTION93
3.0528-3.10280.3381420.27542578X-RAY DIFFRACTION97
3.1028-3.15630.29111310.27142535X-RAY DIFFRACTION97
3.1563-3.21370.30861410.2452594X-RAY DIFFRACTION98
3.2137-3.27550.26911360.24812714X-RAY DIFFRACTION98
3.2755-3.34230.29241260.22632565X-RAY DIFFRACTION99
3.3423-3.4150.26131320.21242635X-RAY DIFFRACTION99
3.415-3.49440.25611300.21192695X-RAY DIFFRACTION100
3.4944-3.58180.2371430.19812640X-RAY DIFFRACTION99
3.5818-3.67860.24541310.19412661X-RAY DIFFRACTION100
3.6786-3.78680.23951560.19552641X-RAY DIFFRACTION100
3.7868-3.9090.22591280.19492615X-RAY DIFFRACTION100
3.909-4.04860.19061500.15982726X-RAY DIFFRACTION100
4.0486-4.21060.17151370.14732607X-RAY DIFFRACTION100
4.2106-4.40210.15551590.13222675X-RAY DIFFRACTION100
4.4021-4.63410.13431380.12592611X-RAY DIFFRACTION100
4.6341-4.92420.14991510.12662658X-RAY DIFFRACTION100
4.9242-5.3040.17341390.13232676X-RAY DIFFRACTION100
5.304-5.8370.17131320.15292693X-RAY DIFFRACTION100
5.837-6.67990.19321600.17652640X-RAY DIFFRACTION100
6.6799-8.40930.20171550.16942627X-RAY DIFFRACTION100
8.4093-49.65880.16821400.16682631X-RAY DIFFRACTION99

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