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- PDB-3sdx: Crystal structure of human autoreactive-Valpha24 NKT TCR in compl... -

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Basic information

Entry
Database: PDB / ID: 3sdx
TitleCrystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • NKT TCR Valpha24 chain
  • NKT TCR autoreactive-Vbeta11 chain
KeywordsIMMUNE SYSTEM / CD1d / autoimmunity / self-recognition / NKT / extracellular
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 / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion ...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 / alpha-beta T cell receptor complex / positive regulation of innate immune response / heterotypic cell-cell adhesion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / beta-2-microglobulin binding / detection of bacterium / cell adhesion molecule binding / positive regulation of T cell proliferation / 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 / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / 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 / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / basolateral plasma membrane / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / lysosome / learning or memory / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma 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
Similarity search - Function
: / MHC-I family domain / T-cell receptor alpha chain, constant 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 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...: / MHC-I family domain / T-cell receptor alpha chain, constant 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 / 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-GCY / T cell receptor alpha chain constant / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.12 Å
AuthorsClarke, A.J. / Patel, O. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2011
Title: Recognition of beta-linked self glycolipids mediated by natural killer T cell antigen receptors
Authors: Pellicci, D.G. / Clarke, A.J. / Patel, O. / Mallevaey, T. / Beddoe, T. / Le Nours, J. / Uldrich, A.P. / McCluskey, J. / Besra, G.S. / Porcelli, S.A. / Gapin, L. / Godfrey, D.I. / Rossjohn, J.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
E: NKT TCR Valpha24 chain
F: NKT TCR autoreactive-Vbeta11 chain
G: NKT TCR Valpha24 chain
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
H: NKT TCR autoreactive-Vbeta11 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,34010
Polymers187,7158
Non-polymers1,6252
Water1,18966
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
E: NKT TCR Valpha24 chain
F: NKT TCR autoreactive-Vbeta11 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6705
Polymers93,8584
Non-polymers8121
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: NKT TCR Valpha24 chain
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
H: NKT TCR autoreactive-Vbeta11 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6705
Polymers93,8584
Non-polymers8121
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.041, 152.337, 85.119
Angle α, β, γ (deg.)90.00, 97.24, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13E
23G
14F
24H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 280
2111C6 - 280
1121B1 - 97
2121D1 - 97
1131E1 - 203
2131G1 - 203
1141F1 - 247
2141H1 - 247

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules ACBDEGFH

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 31344.336 Da / Num. of mol.: 2 / Fragment: extracellular domain, UNP residues 24-295
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pFastBac dual / Cell line (production host): Hi5 / 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.: 2 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pFastBac dual / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769
#3: Protein NKT TCR Valpha24 chain


Mass: 22664.006 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: P01848*PLUS
#4: Protein NKT TCR autoreactive-Vbeta11 chain


Mass: 28101.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): RIL

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Non-polymers , 2 types, 68 molecules

#5: Chemical ChemComp-GCY / N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide / beta-Galactosylceramide, Ceramide beta-D-galactoside


Mass: 812.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C48H93NO8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 400, 0.1M Tris, 0.1M MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.12→122.77 Å / Num. obs: 46742 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 60.377 Å2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→122.77 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.85 / Occupancy max: 1 / Occupancy min: 0.34 / SU B: 23.36 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2362 5.1 %RANDOM
Rwork0.2319 ---
obs0.234 46742 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 124.66 Å2 / Biso mean: 61.5591 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å2-3.24 Å2
2---3.77 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 3.12→122.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12668 0 90 66 12824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113121
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9317869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00751597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03723.947603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.999152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7841571
X-RAY DIFFRACTIONr_chiral_restr0.080.21945
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110057
X-RAY DIFFRACTIONr_mcbond_it0.6281.58038
X-RAY DIFFRACTIONr_mcangle_it1.183212955
X-RAY DIFFRACTIONr_scbond_it1.07935083
X-RAY DIFFRACTIONr_scangle_it1.9624.54913
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2104TIGHT POSITIONAL0.040.05
1A2104TIGHT THERMAL0.060.5
2B775TIGHT POSITIONAL0.030.05
2B775TIGHT THERMAL0.040.5
3E1482TIGHT POSITIONAL0.040.05
3E1482TIGHT THERMAL0.070.5
4F1865TIGHT POSITIONAL0.040.05
4F1865TIGHT THERMAL0.060.5
LS refinement shellResolution: 3.118→3.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 140 -
Rwork0.317 2902 -
all-3042 -
obs--88.05 %

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