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- PDB-6cug: Crystal structure of BC8B TCR-CD1b-PC complex -

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Basic information

Entry
Database: PDB / ID: 6cug
TitleCrystal structure of BC8B TCR-CD1b-PC complex
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1b
KeywordsIMMUNE SYSTEM / T cell receptor / antigen presenting molecule / CD1b / PC / phosphatidylcholine
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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport ...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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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
tetracosyl octadecanoate / Chem-POV / T-cell surface glycoprotein CD1b / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsShahine, A.E. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2019
Title: A T-cell receptor escape channel allows broad T-cell response to CD1b and membrane phospholipids.
Authors: Shahine, A. / Reinink, P. / Reijneveld, J.F. / Gras, S. / Holzheimer, M. / Cheng, T.Y. / Minnaard, A.J. / Altman, J.D. / Lenz, S. / Prandi, J. / Kubler-Kielb, J. / Moody, D.B. / Rossjohn, J. / Van Rhijn, I.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 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 1.3Jun 5, 2024Group: Data collection / Category: refln
Revision 1.4Oct 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
A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
D: T-cell receptor alpha variable TRAV9-2 - BC8B TCR
E: T-cell receptor beta variable TRBV6-2 - BC8B TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2428
Polymers95,6044
Non-polymers1,6384
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.300, 65.700, 101.900
Angle α, β, γ (deg.)90.000, 100.700, 90.000
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): 293S GnTI / Organ (production host): Kidney / Production host: Homo sapiens (human) / Strain (production host): HEK / Tissue (production host): embryonic kidney / 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 (production host): epithelial kidney / Cell line (production host): 293S GnTI / Organ (production host): Kidney / Production host: Homo sapiens (human) / Strain (production host): HEK / References: UniProt: P61769

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

#3: Protein T-cell receptor alpha variable TRAV9-2 - BC8B TCR


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 (E. coli) / Strain (production host): BL21(DE3)
#4: Protein T-cell receptor beta variable TRBV6-2 - BC8B TCR


Mass: 27598.873 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 (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 1 types, 1 molecules

#5: 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: 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 , 4 types, 417 molecules

#6: Chemical ChemComp-CUY / tetracosyl octadecanoate


Mass: 621.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H84O2
#7: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.52 Å3/Da / Density % sol: 51.23 % / Description: cubic
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: PEG 3350, Tris-HCl / PH range: 7.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2017
RadiationMonochromator: Channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→65.7 Å / Num. obs: 78785 / % possible obs: 100 % / Redundancy: 14.3 % / Biso Wilson estimate: 40.66 Å2 / CC1/2: 0.903 / Rpim(I) all: 0.0178 / Net I/σ(I): 5.2
Reflection scaleGroup code: 1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 14.4 % / Num. unique obs: 5464 / CC1/2: 0.5 / Rpim(I) all: 0.0465 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WL1, 4QRP, 4G8F

5wl1

4qrp

4g8f


Resolution: 2.4→54.93 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.874 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.234
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1889 5.04 %RANDOM
Rwork0.187 ---
obs0.189 37517 100 %-
Displacement parametersBiso max: 106.94 Å2 / Biso mean: 32.6 Å2 / Biso min: 5.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.4808 Å20 Å2-3.3234 Å2
2---12.2613 Å20 Å2
3---6.7805 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.4→54.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 103 414 6793
Biso mean--39.72 31.97 -
Num. residues----803
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2979SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes160HARMONIC2
X-RAY DIFFRACTIONt_gen_planes953HARMONIC5
X-RAY DIFFRACTIONt_it6579HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion827SEMIHARMONIC5
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_contact7307SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6579HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8931HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion2.96
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.258 143 4.91 %
Rwork0.232 2768 -
all0.233 2911 -
obs--99.93 %
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)
10.39370.8051-0.75960.04220.35550.4951-0.00080.00120.0092-0.00720.0019-0.0018-0.0017-0.0042-0.0011-0.0011-0.03490.0053-0.0019-0.0155-0.0107-29.1406-8.330815.776
20.3565-0.12-0.365200.29970.0169-0.0032-0.00720.0018-0.0024-0.0008-0.00660.0167-0.00060.0040.0092-0.00250.0052-0.0057-0.0175-0.0055-24.9817-20.140217.8087
30.15170.21610.07170.00050.53710.4427-0.0012-0.0057-0.00270.00440.00350.01120.0033-0.0044-0.0023-0.0122-0.0029-0.0080.0184-0.0216-0.0112-46.7688-3.782646.5175
40.1898-0.00670.17540.07530.20220.1104-0.00220.00680.0057-0.00010.00510.0025-0.0031-0.0136-0.0029-0.01220.01140.00230.0114-0.0073-0.0012-50.19360.746326.0167
50.1135-0.7273-0.09310.1969-0.05320.2741-0.0006-0.0029-0.00570.0028-0.0054-0.01060.004-0.00130.00590.00390.02640.0051-0.0131-0.02560.0052-3.8814-18.286-10.4942
60.1982-0.3533-0.16750.11930.1830.10690.00040.00270.0026-0.0014-0.0008-0.00370.00160.00040.0004-0.0130.0130.00810.0096-0.0078-0.001411.6988-8.0054-38.7968
7-0.08110.3130.16260.2329-0.3360.55170.00080.0033-0.00010.00560.00640.0033-0.0053-0.0049-0.00720.00660.0101-0.0075-0.00830.0063-0.0024-14.0732.0696-11.9898
80.3115-0.1298-0.17590.09970.01270.18890.00870.013-0.0066-0.0006-0.0067-0.001-0.00360.0214-0.002-0.0127-0.0068-0.0080.0072-0.0113-0.0108-0.61672.0632-39.5397
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 109}A3 - 109
2X-RAY DIFFRACTION2{A|110 - 175}A110 - 175
3X-RAY DIFFRACTION3{A|176 - 278}A176 - 278
4X-RAY DIFFRACTION4{B|3 - 99}B3 - 99
5X-RAY DIFFRACTION5{D|1 - 114}D1 - 114
6X-RAY DIFFRACTION6{D|115 - 187}D115 - 190
7X-RAY DIFFRACTION7{E|2 - 115}E2 - 115
8X-RAY DIFFRACTION8{E|116 - 245}E116 - 245

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