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- PDB-4ww2: Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Cha... -

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Basic information

Entry
Database: PDB / ID: 4ww2
TitleCrystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • TCR Alpha Chain-TRAV21-TRAJ8
  • TCR Beta Chain-TRBV7-8
KeywordsIMMUNE SYSTEM / Natural Killer T Cells / Immunity
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 / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion ...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 / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion / T cell receptor complex / beta-2-microglobulin binding / alpha-beta T cell activation / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / 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 / response to bacterium / 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 / T cell receptor signaling pathway / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / basolateral plasma membrane / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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 / cytoplasm
Similarity search - Function
: / MHC-I family domain / Domain of unknown function (DUF1968) / : / 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-I family domain / Domain of unknown function (DUF1968) / : / 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/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-JLS / T cell receptor alpha variable 21 / T cell receptor beta constant 2 / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLe Nours, J. / Praveena, T. / Pellicci, D. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. ...Le Nours, J. / Praveena, T. / Pellicci, D. / Gherardin, N.A. / Lim, R.T. / Besra, G. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
CitationJournal: Nat Commun / Year: 2016
Title: Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens.
Authors: Le Nours, J. / Praveena, T. / Pellicci, D.G. / Gherardin, N.A. / Ross, F.J. / Lim, R.T. / Besra, G.S. / Keshipeddy, S. / Richardson, S.K. / Howell, A.R. / Gras, S. / Godfrey, D.I. / Rossjohn, J. / Uldrich, A.P.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 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 1.3Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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: TCR Alpha Chain-TRAV21-TRAJ8
B: TCR Beta Chain-TRBV7-8
C: Antigen-presenting glycoprotein CD1d
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2867
Polymers94,0154
Non-polymers1,2713
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.990, 46.300, 124.650
Angle α, β, γ (deg.)90.00, 122.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABCF

#1: Protein TCR Alpha Chain-TRAV21-TRAJ8


Mass: 22573.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J279*PLUS
#2: Protein TCR Beta Chain-TRBV7-8


Mass: 27368.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B9*PLUS
#3: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 32324.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15813
#4: 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: pFastBac Dual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769

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Sugars , 1 types, 2 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.: 2 / 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 , 2 types, 171 molecules

#6: Chemical ChemComp-JLS / (15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]tetracos-15-enamide / PBS-44


Mass: 828.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H93NO9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 9-10% PEG 6K 0.1M MES 6.0 4% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.7108 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7108 Å / Relative weight: 1
ReflectionResolution: 2.48→44.8 Å / Num. obs: 36324 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 51.78 Å2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.6 / % possible all: 97.3

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2PO6, 4WW1

2po6

4ww1


Resolution: 2.48→44.8 Å / Cor.coef. Fo:Fc: 0.9347 / Cor.coef. Fo:Fc free: 0.8972 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.257
RfactorNum. reflection% reflectionSelection details
Rfree0.2439 1815 5 %RANDOM
Rwork0.1957 ---
obs0.1981 36324 99.26 %-
Displacement parametersBiso mean: 56.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.789 Å20 Å2-0.2764 Å2
2---1.6818 Å20 Å2
3---0.8929 Å2
Refine analyzeLuzzati coordinate error obs: 0.394 Å
Refinement stepCycle: LAST / Resolution: 2.48→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6284 0 86 170 6540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086550HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.038938HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2935SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes967HARMONIC5
X-RAY DIFFRACTIONt_it6550HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion2.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion856SEMIHARMONIC5
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_contact7043SEMIHARMONIC4
LS refinement shellResolution: 2.48→2.55 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2957 178 6.32 %
Rwork0.247 2640 -
all0.2502 2818 -
obs--99.26 %
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)
13.7317-1.0246-0.88930.39330.36623.40430.03610.40050.1274-0.1331-0.12570.1467-0.0869-0.19630.0896-0.0058-0.12-0.0195-0.23320.0275-0.047234.4937-12.4426-21.8917
22.8926-0.65140.0930.38150.64861.2869-0.0066-0.1155-0.0482-0.01390.01420.1315-0.06170.1153-0.0076-0.0627-0.0002-0.0273-0.24450.0073-0.066845.108-23.2759-10.1966
32.350.3331-1.65090.5059-0.0861.02430.1244-0.7251-0.03540.14890.0011-0.09520.02630.4356-0.1254-0.19950.064-0.0030.3327-0.1033-0.25293.2486-8.416328.3926
4-0.15520.5759-1.19663.7144-2.18095.31320.2735-0.4411-0.71650.46860.2382-0.30480.5380.2459-0.5116-0.40080.0763-0.19290.56870.2278-0.3023.1366-17.701645.2713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ F|* }

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