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- PDB-8t4z: T-cell receptor and lipid complex structure -

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Basic information

Entry
Database: PDB / ID: 8t4z
TitleT-cell receptor and lipid complex structure
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Beta-chain, T cell receptor beta chain MC.7.G5 chimera
  • T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera
KeywordsLIPID BINDING PROTEIN / MHC-like protein / antigen-presenting molecule
Function / homology
Function and homology information


detection of tumor cell / regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 ...detection of tumor cell / regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 / alpha-beta T cell receptor complex / positive regulation of macrophage activation / positive thymic T cell selection / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell mediated cytotoxicity directed against tumor cell target / T cell receptor complex / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / response to bacterium / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / sensory perception of smell / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / positive regulation of cellular senescence / positive regulation of type II interferon production / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / late endosome / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / signaling receptor activity / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / lysosome / early endosome / learning or memory / cell surface receptor signaling pathway / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-Type / : / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...: / : / : / MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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
Similarity search - Domain/homology
: / T cell receptor alpha variable 11 / Beta-chain / Human nkt tcr alpha chain / Beta-2-microglobulin / T cell receptor beta chain MC.7.G5 / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.691 Å
AuthorsPraveena, T. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells.
Authors: Cheng, T.Y. / Praveena, T. / Govindarajan, S. / Almeida, C.F. / Pellicci, D.G. / Arkins, W.C. / Van Rhijn, I. / Venken, K. / Elewaut, D. / Godfrey, D.I. / Rossjohn, J. / Moody, D.B.
History
DepositionJun 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d1
B: Beta-2-microglobulin
C: T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera
D: Beta-chain, T cell receptor beta chain MC.7.G5 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4618
Polymers96,2164
Non-polymers2,2464
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.906, 79.036, 242.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P11609
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein T cell receptor alpha variable 11, Human nkt tcr alpha chain chimera / T cell receptor alpha variable 11D / Human nkt tcr beta chain


Mass: 22779.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav11, Trav11d, B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J1J9, UniProt: K7N5M3
#4: Protein Beta-chain, T cell receptor beta chain MC.7.G5 chimera / TR beta chain TRBV25-1*01J2S3*01C2*01 / MC.7.G5 TRB


Mass: 27113.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TRB / Production host: Escherichia coli (E. coli) / References: UniProt: A2NTY6, UniProt: P0DTU4

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Sugars , 2 types, 3 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.: 2
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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 27 molecules

#7: Chemical ChemComp-Y73 / N-[(2R,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide


Mass: 648.097 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 18-20% PEG3350, 8% Tacsimate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.69→48.47 Å / Num. obs: 31771 / % possible obs: 99.6 % / Redundancy: 7.3 % / Rpim(I) all: 0.04 / Net I/σ(I): 12.5
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 4050 / Rpim(I) all: 0.332

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: 000)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.691→48.087 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1597 5.04 %
Rwork0.1929 --
obs0.1966 31680 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.691→48.087 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6471 0 152 26 6649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016815
X-RAY DIFFRACTIONf_angle_d1.1729306
X-RAY DIFFRACTIONf_dihedral_angle_d16.6744007
X-RAY DIFFRACTIONf_chiral_restr0.061035
X-RAY DIFFRACTIONf_plane_restr0.0071191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.691-2.77770.391480.30292581X-RAY DIFFRACTION96
2.7777-2.87690.41081300.28632706X-RAY DIFFRACTION100
2.8769-2.99210.41391540.26832678X-RAY DIFFRACTION100
2.9921-3.12820.32981490.24592686X-RAY DIFFRACTION100
3.1282-3.29310.32361510.23362718X-RAY DIFFRACTION100
3.2931-3.49940.2761240.19652744X-RAY DIFFRACTION100
3.4994-3.76950.27451310.19162745X-RAY DIFFRACTION100
3.7695-4.14870.23541570.16892741X-RAY DIFFRACTION100
4.1487-4.74850.20811370.1372748X-RAY DIFFRACTION100
4.7485-5.98080.21131610.16182792X-RAY DIFFRACTION100
5.9808-48.0870.25851550.20442944X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -0.3723 Å / Origin y: -0.7787 Å / Origin z: 58.1576 Å
111213212223313233
T0.5077 Å20.0334 Å2-0.0186 Å2-0.303 Å2-0.0182 Å2--0.4676 Å2
L0.5812 °20.1342 °21.3225 °2--0.155 °20.3503 °2--3.8356 °2
S0.0082 Å °-0.0376 Å °0.0195 Å °-0.0179 Å °-0.016 Å °0.018 Å °0.03 Å °-0.0229 Å °0.0017 Å °
Refinement TLS groupSelection details: all

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