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- PDB-6c09: Ternary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex -

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Basic information

Entry
Database: PDB / ID: 6c09
TitleTernary crystal structure of the 3C8 TCR-CD1c-monoacylglycerol complex
Components
  • (3C8 T cell receptor ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • T-cell surface glycoprotein CD1c
KeywordsIMMUNE SYSTEM / T cell Receptor / Antigen Presentation
Function / homology
Function and homology information


glycolipid binding / T cell activation involved in immune response / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen ...glycolipid binding / T cell activation involved in immune response / 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 ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...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
DECANE / (2R)-2,3-dihydroxypropyl hexadecanoate / : / DI(HYDROXYETHYL)ETHER / T-cell surface glycoprotein CD1c / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsWun, K.S. / Rossjohn, J.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
Australian Research Council (ARC) Australia
Citation
Journal: Nat. Immunol. / Year: 2018
Title: T cell autoreactivity directed toward CD1c itself rather than toward carried self lipids.
Authors: Wun, K.S. / Reijneveld, J.F. / Cheng, T.Y. / Ladell, K. / Uldrich, A.P. / Le Nours, J. / Miners, K.L. / McLaren, J.E. / Grant, E.J. / Haigh, O.L. / Watkins, T.S. / Suliman, S. / Iwany, S. / ...Authors: Wun, K.S. / Reijneveld, J.F. / Cheng, T.Y. / Ladell, K. / Uldrich, A.P. / Le Nours, J. / Miners, K.L. / McLaren, J.E. / Grant, E.J. / Haigh, O.L. / Watkins, T.S. / Suliman, S. / Iwany, S. / Jimenez, J. / Calderon, R. / Tamara, K.L. / Leon, S.R. / Murray, M.B. / Mayfield, J.A. / Altman, J.D. / Purcell, A.W. / Miles, J.J. / Godfrey, D.I. / Gras, S. / Price, D.A. / Van Rhijn, I. / Moody, D.B. / Rossjohn, J.
#1: Journal: To Be Published
Title: To be added later
Authors: Wun, K.S. / Rossjohn, J.
History
DepositionDec 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.pdbx_host_org_cell_line
Revision 1.2Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 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 1.5Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1c
B: Beta-2-microglobulin
C: 3C8 T cell receptor alpha-chain
D: 3C8 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,71015
Polymers95,4644
Non-polymers1,24611
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, The assembly broadly follows that of previously established T cell receptor - MHC complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11830 Å2
ΔGint-16 kcal/mol
Surface area36110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.170, 173.170, 82.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1c


Mass: 32283.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P29017
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 12646.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P61769

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3C8 T cell receptor ... , 2 types, 2 molecules CD

#3: Protein 3C8 T cell receptor alpha-chain


Mass: 22947.650 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#4: Protein 3C8 T cell receptor beta-chain


Mass: 27587.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)

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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 / N-Acetylglucosamine


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 , 6 types, 23 molecules

#6: Chemical ChemComp-EKG / (2R)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O4
#7: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 3.85 Å3/Da / Density % sol: 68.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% PEG 3350, 0.2M potassium thiocynate

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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: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.95→80 Å / Num. obs: 30233 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 99.46 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4343 / CC1/2: 0.15 / Rpim(I) all: 0.76 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OV6, 1BD2

3ov6

1bd2


Resolution: 2.95→37.53 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.503 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.278
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1530 5.07 %RANDOM
Rwork0.174 ---
obs0.176 30198 100 %-
Displacement parametersBiso mean: 92.29 Å2
Baniso -1Baniso -2Baniso -3
1--5.1962 Å20 Å20 Å2
2---5.1962 Å20 Å2
3---10.3924 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.95→37.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6125 0 79 13 6217
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016403HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.188719HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2060SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes131HARMONIC2
X-RAY DIFFRACTIONt_gen_planes957HARMONIC5
X-RAY DIFFRACTIONt_it6403HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion19.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion824SEMIHARMONIC5
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_contact6864SEMIHARMONIC4
LS refinement shellResolution: 2.95→3.05 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2965 130 4.45 %
Rwork0.2406 2792 -
all0.243 2922 -
obs--99.97 %
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)
15.8849-3.02932.40793.0614-1.78182.4864-0.16340.49680.3139-0.0205-0.0975-0.3704-0.11530.4920.2609-0.08550.1940.0074-0.1204-0.021-0.287396.9147-27.2621-21.9431
24.84140.09560.03933.36880.28496.9493-0.0338-0.0264-0.3199-0.06640.0501-0.3442-0.14860.6622-0.0163-0.00230.1962-0.0144-0.02830.0576-0.1279122.8123-45.1833-0.3454
34.2392-0.0733-0.61373.2147-0.04834.24170.14310.4234-1.0804-0.3496-0.04970.18960.8412-0.0348-0.0934-0.00770.2545-0.1265-0.1139-0.1553-0.0011107.909-51.5759-14.5674
43.1256-0.73881.69844.87250.31453.1170.1528-0.08110.0056-0.0746-0.11950.07040.11390.1517-0.03330.1110.0240.054-0.1198-0.0087-0.215575.6646-3.8155-23.7592
53.571-1.08-0.04422.85760.16290.9028-0.0215-0.40660.14910.53570.06260.6546-0.4619-0.5644-0.04110.01750.30920.19780.09470.10160.056746.51112.8854-29.9859
610.3172-0.2731.53812.674-1.94653.86930.2411-0.463-0.77380.21550.20110.27460.5175-0.3225-0.44220.1801-0.02-0.0369-0.22910.0308-0.21865.9422-22.8108-31.4745
71.67351.8109-0.57076.4481-0.71952.5964-0.2651-0.13970.1447-0.00070.45231.1507-0.1439-1.02-0.1873-0.24910.0476-0.00170.10740.2333-0.003645.73450.6096-40.6732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|7 - A|187 A|302 - A|302 A|303 - A|303 A|304 - A|304 }A7 - 187
2X-RAY DIFFRACTION1{ A|7 - A|187 A|302 - A|302 A|303 - A|303 A|304 - A|304 }A302
3X-RAY DIFFRACTION1{ A|7 - A|187 A|302 - A|302 A|303 - A|303 A|304 - A|304 }A303
4X-RAY DIFFRACTION1{ A|7 - A|187 A|302 - A|302 A|303 - A|303 A|304 - A|304 }A304
5X-RAY DIFFRACTION2{ A|188 - A|279 }A188 - 279
6X-RAY DIFFRACTION3{ B|2 - B|99 }B2 - 99
7X-RAY DIFFRACTION4{ C|2 - C|110 }C2 - 110
8X-RAY DIFFRACTION5{ C|111 - C|199 }C111 - 199
9X-RAY DIFFRACTION6{ D|3 - D|117 }D3 - 117
10X-RAY DIFFRACTION7{ D|118 - D|246 }D118 - 246

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