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- PDB-3vwk: Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha... -

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Basic information

Entry
Database: PDB / ID: 3vwk
TitleTernary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide complex
Components
  • (NKT15 T cell receptor ...) x 2
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / CD1D / NKT T CELL RECEPTOR / ALPHA-GALACTOSYLCERAMIDE / PROTEIN RECEPTOR COMPLEX / CELL MEMBRANE / DISULFIDE BOND / ENDOSOME / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE / IMMUNOGLOBULIN DOMAIN / INNATE IMMUNITY / LYSOSOME / MEMBRANE / TRANSMEMBRANE / DISEASE MUTATION / GLYCATION / MHC I / PYRROLIDONE CARBOXYLIC ACID / SECRETED
Function / homology
Function and homology information


lipid antigen binding / T cell selection / 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 innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding ...lipid antigen binding / T cell selection / 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 innate immune response / heterotypic cell-cell adhesion / beta-2-microglobulin binding / detection of bacterium / positive regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / histone binding / T cell differentiation in thymus / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / 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 / cytoplasm / 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
Chem-4GH / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.935 Å
AuthorsWun, K.S. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Human and mouse type I natural killer T cell antigen receptors exhibit different fine specificities for CD1d-antigen complex
Authors: Wun, K.S. / Ross, F. / Patel, O. / Besra, G.S. / Porcelli, S.A. / Richardson, S.K. / Keshipeddy, S. / Howell, A.R. / Godfrey, D.I. / Rossjohn, J.
History
DepositionAug 24, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Structure summary
Revision 1.2Aug 14, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 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

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
C: NKT15 T cell receptor alpha-chain
D: NKT15 T cell receptor beta-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6268
Polymers95,3334
Non-polymers1,2934
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.270, 177.260, 83.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 32324.383 Da / Num. of mol.: 1 / Fragment: UNP residues 21-295
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
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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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NKT15 T cell receptor ... , 2 types, 2 molecules CD

#3: Protein NKT15 T cell receptor alpha-chain


Mass: 23227.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein NKT15 T cell receptor beta-chain


Mass: 28033.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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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: 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 , 3 types, 22 molecules

#6: Chemical ChemComp-4GH / N-{(2S,3R)-1-[(4-deoxy-alpha-D-xylo-hexopyranosyl)oxy]-3-hydroxyoctadecan-2-yl}hexacosanamide


Mass: 826.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C50H99NO7
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 9% PEG 10000, 0.2M magnesium chloride, 0.1M glycine, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2009
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→80 Å / Num. obs: 22894 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 64.7 Å2 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.9-3.067.72.432781100
9.17-806.728.5801199.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HUJ
Resolution: 2.935→60.872 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.32 / σ(F): 1.38 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1182 5.17 %RANDOM
Rwork0.1909 ---
all0.1939 22883 --
obs0.1939 22883 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.13 Å2 / Biso mean: 71.8605 Å2 / Biso min: 29.77 Å2
Refinement stepCycle: LAST / Resolution: 2.935→60.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5991 0 87 20 6098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056260
X-RAY DIFFRACTIONf_angle_d0.9038534
X-RAY DIFFRACTIONf_dihedral_angle_d14.5632163
X-RAY DIFFRACTIONf_chiral_restr0.06951
X-RAY DIFFRACTIONf_plane_restr0.0031086
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9354-3.06890.28641240.2343229684
3.0689-3.23070.29031440.23092726100
3.2307-3.43310.27431610.21252725100
3.4331-3.69820.26611590.19252750100
3.6982-4.07030.25241580.18132734100
4.0703-4.65910.20561490.15122769100
4.6591-5.86920.22441350.16772799100
5.8692-60.88540.25881520.2141290299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.88340.80531.02433.77951.26554.44060.3272-0.103-0.31910.2888-0.09070.04320.80660.0748-0.21430.52-0.0421-0.14970.3969-0.01160.359417.9638-61.859646.3648
25.4029-0.2654-2.98421.7048-0.44855.8517-0.17380.4556-0.2442-0.19720.655-0.48191.64341.1146-0.46081.01480.2532-0.30050.9945-0.38840.763519.7945-78.495114.3868
32.81421.24952.8492.88711.04937.7353-0.05640.77820.0462-0.27020.09560.217-0.1710.6606-0.06760.41890.0718-0.10920.6653-0.11270.40712.1397-60.12418.6445
43.8739-0.7365-3.67283.2152.74928.07430.1592-0.4319-0.02080.2096-0.0346-0.03130.1976-0.1946-0.14010.26-0.0814-0.03010.49490.02670.36310.977-44.140876.8832
54.5203-0.0811-2.24036.0275-4.04437.25320.4503-0.27830.82971.1167-0.16571.0436-0.5513-0.5264-0.25650.7494-0.21310.27340.8565-0.37130.97045.997-17.222298.8426
64.7385-1.59970.25287.92653.02794.56580.244-0.04090.5940.2593-0.17960.2102-0.3659-0.1901-0.07940.3482-0.06410.14670.39550.00410.485624.9515-29.602965.544
72.17481.1479-0.41336.244-2.77974.45410.1457-0.66460.34820.517-0.1955-0.7562-0.19160.15190.10230.5293-0.09850.03550.872-0.51511.143422.5481-13.545192.0418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:182)A7 - 182
2X-RAY DIFFRACTION2(chain A and resid 183:277)A183 - 277
3X-RAY DIFFRACTION3(chain B and resid 2:97)B2 - 97
4X-RAY DIFFRACTION4(chain C and resid 2:116)C2 - 116
5X-RAY DIFFRACTION5(chain C and resid 117:204)C117 - 204
6X-RAY DIFFRACTION6(chain D and resid 3:119)D3 - 119
7X-RAY DIFFRACTION7(chain D and resid 120:246)D120 - 246

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