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- PDB-8dv4: Crystal structure of the BC8B TCR-CD1b-PI complex -

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Basic information

Entry
Database: PDB / ID: 8dv4
TitleCrystal structure of the BC8B TCR-CD1b-PI complex
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1b
KeywordsIMMUNE SYSTEM / Antigen presentation / TCR / autoreactivity
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / learning or memory / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / 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 ...MHC-I family domain / 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 / Mainly Beta
Similarity search - Domain/homology
tetracosyl octadecanoate / alpha-D-mannopyranose / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / T-cell surface glycoprotein CD1b / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFarquhar, R. / Rossjohn, J. / Shahine, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE210101031 Australia
CitationJournal: J.Biol.Chem. / Year: 2023
Title: alpha beta T-cell receptor recognition of self-phosphatidylinositol presented by CD1b.
Authors: Farquhar, R. / Van Rhijn, I. / Moody, D.B. / Rossjohn, J. / Shahine, A.
History
DepositionJul 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
D: T-cell receptor alpha variable TRAV9-2
E: T-cell receptor beta variable TRBV6-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,53024
Polymers95,6044
Non-polymers3,92620
Water4,450247
1
A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,04915
Polymers45,2792
Non-polymers2,77013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-42 kcal/mol
Surface area19290 Å2
MethodPISA
2
D: T-cell receptor alpha variable TRAV9-2
E: T-cell receptor beta variable TRBV6-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4809
Polymers50,3252
Non-polymers1,1557
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-35 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.088, 65.430, 101.581
Angle α, β, γ (deg.)90.00, 102.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1b


Mass: 33530.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1B / Plasmid: pHLSEC / Cell line (production host): HEK392S / Production host: Homo sapiens (human) / References: UniProt: P29016
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHLSEC / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P61769

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T-cell receptor ... , 2 types, 2 molecules DE

#3: Protein T-cell receptor alpha variable TRAV9-2


Mass: 22726.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
#4: Protein T-cell receptor beta variable TRBV6-2


Mass: 27598.873 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)

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Sugars , 4 types, 4 molecules

#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#10: 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.: 1 / Source method: obtained synthetically / 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 , 7 types, 263 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-CUY / tetracosyl octadecanoate


Mass: 621.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H84O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#13: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#14: Chemical ChemComp-PIE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL


Mass: 836.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H80O13P / Feature type: SUBJECT OF INVESTIGATION
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 24 %(w/v) PEG 4000, 0.02 M Tris-HCl (pH 7.0), 2% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→46.07 Å / Num. obs: 36933 / % possible obs: 99.88 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rpim(I) all: 0.059 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3651 / CC1/2: 0.87 / Rpim(I) all: 0.588 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CUG

6cug


Resolution: 2.4→46.07 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 1858 5.04 %
Rwork0.1915 --
obs0.1947 36854 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6223 0 251 248 6722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076646
X-RAY DIFFRACTIONf_angle_d0.9659010
X-RAY DIFFRACTIONf_dihedral_angle_d16.2412419
X-RAY DIFFRACTIONf_chiral_restr0.053998
X-RAY DIFFRACTIONf_plane_restr0.0081139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.40431500.30732647X-RAY DIFFRACTION100
2.46-2.540.36831540.29532676X-RAY DIFFRACTION100
2.54-2.620.33381550.26842638X-RAY DIFFRACTION99
2.62-2.710.37291240.25682703X-RAY DIFFRACTION100
2.71-2.820.32691150.24332702X-RAY DIFFRACTION100
2.82-2.950.34191460.22842659X-RAY DIFFRACTION100
2.95-3.110.28351360.22672693X-RAY DIFFRACTION100
3.11-3.30.32091450.21852674X-RAY DIFFRACTION100
3.3-3.550.29871480.19452677X-RAY DIFFRACTION100
3.56-3.910.26171480.18062719X-RAY DIFFRACTION100
3.91-4.480.19291330.15042715X-RAY DIFFRACTION100
4.48-5.640.18331470.14632714X-RAY DIFFRACTION100
5.64-46.070.20091570.17022779X-RAY DIFFRACTION100

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