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- PDB-9rse: Human CD1d with lipid antigen bound -

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Basic information

Entry
Database: PDB / ID: 9rse
TitleHuman CD1d with lipid antigen bound
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / CD1d / lipopeptide / lipid antigen / iNKT
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 / lipopeptide binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / 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 / lipopeptide binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / 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 / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of iron ion transport / 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 / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / basolateral plasma membrane / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal membrane / 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 exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
MHC-I family domain / 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-AGH / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsBurns, D. / Maly, M. / Tews, I. / Mansour, S.
Funding support United Kingdom, 6items
OrganizationGrant numberCountry
University of Southampton United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W007045/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/P023754/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W025728/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S024220/1 United Kingdom
Cancer Research UK23562 United Kingdom
CitationJournal: To Be Published
Title: Structural features of human and macaque CD1d: Implications for antigen presentation
Authors: Burns, D. / Look, A. / Turner, S. / Maly, M. / Essex, J.W. / Tews, I. / Mansour, S.
History
DepositionJul 1, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2026Provider: 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
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9158
Polymers90,7224
Non-polymers2,1934
Water12,592699
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4584
Polymers45,3612
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-32 kcal/mol
Surface area18950 Å2
MethodPISA
2
C: Antigen-presenting glycoprotein CD1d
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4584
Polymers45,3612
Non-polymers1,0972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-31 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.6218, 156.3734, 51.9093
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 33481.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta DE3 / References: UniProt: P15813
#2: Protein Beta-2-microglobulin


Mass: 11879.356 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 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3 / References: UniProt: P61769
#3: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C50H99NO9 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0. ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9253 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.76→49.27 Å / Num. obs: 92489 / % possible obs: 96.62 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.95 Å2 / CC1/2: 0.968 / CC star: 0.992 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Net I/σ(I): 14.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3363 / CC1/2: 0.532 / CC star: 0.833 / Rpim(I) all: 0.487 / Rrim(I) all: 0.937 / % possible all: 71.07

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Processing

Software
NameVersionClassification
xia2data scaling
DIALS3.21data reduction
gemmi0.7.1data extraction
MOLREPphasing
Coot0.9.8.96model building
Servalcat0.4.113refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→49.266 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2542 2016 -
Rwork0.2132 90307 -
obs-92323 96.44 %
Displacement parametersBiso mean: 35.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.77060556 Å20 Å20 Å2
2---1.06836745 Å20 Å2
3----3.70223811 Å2
Refinement stepCycle: LAST / Resolution: 1.76→49.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6028 0 152 699 6879
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.013267250.0119
X-RAY DIFFRACTIONs_angle_nonh_deg2.082291751.8177
X-RAY DIFFRACTIONs_dihedral_angle_1_deg7.32648295
X-RAY DIFFRACTIONs_dihedral_angle_2_deg4.94072335
X-RAY DIFFRACTIONs_dihedral_angle_3_deg11.7448219910
X-RAY DIFFRACTIONs_dihedral_angle_6_deg15.181739710
X-RAY DIFFRACTIONs_chiral_restr0.09389530.1326
X-RAY DIFFRACTIONs_planes0.015297840.02
X-RAY DIFFRACTIONs_nbd0.221694780.2
X-RAY DIFFRACTIONs_nbtor0.2238111220.2
X-RAY DIFFRACTIONs_hbond_nbd0.1826820.2
X-RAY DIFFRACTIONs_symmetry_nbd0.21511590.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.1926150.2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkCor.coef. Fo:FcCor.coef. Fo:Fc freeNum. reflection obs% reflection obs (%)
1.76-1.790.3936680.412732550.66070.6314332370.78
1.79-1.8220.5537990.442943920.67480.503449198.51
1.822-1.8550.42211050.413943860.71050.7625449198.68
1.855-1.8910.43381000.387542490.72690.674434998.35
1.891-1.9280.39841080.360141890.76060.6035429798.4
1.928-1.9680.4479800.327140900.77650.6349417098.26
1.968-2.010.3385910.274740020.81070.7195409397.24
2.01-2.0550.2977970.250239200.85320.823401798.67
2.055-2.1030.2732890.228438880.87540.7753397798.95
2.103-2.1550.3186770.21538230.88860.7401390098.63
2.155-2.2110.2662960.222336700.88380.7962376698.77
2.211-2.2720.2654750.216236020.89320.8421367798.26
2.272-2.3370.2521580.208835360.890.8243359498.93
2.337-2.4090.2771760.203933570.89490.7711343397.25
2.409-2.4880.2544730.199432890.89760.8314336298.3
2.488-2.5750.2603680.187432150.90910.847328398.53
2.575-2.6720.2608600.183830540.9090.8588311497.96
2.672-2.7810.234620.182729620.91340.8483302497.58
2.781-2.9040.2856600.192928680.90310.8037292897.83
2.904-3.0450.2505690.197427130.90170.8247278297.75
3.045-3.2090.1997600.189625730.91210.8861263396.8
3.209-3.4030.1992580.182424310.92240.8844248997.53
3.403-3.6370.2455450.177423050.93060.8633235096.67
3.637-3.9260.1902460.181521430.91670.9326218995.92
3.926-4.2980.209460.15919710.92940.855201796.05
4.298-4.8010.1803420.155717820.93020.9261182495.45
4.801-5.5350.1969350.170615940.9210.8718162995.54
5.535-6.7580.2003330.239313490.87280.9182138294.21
6.758-9.4680.2407220.264610530.85960.8817107592.99
9.468-49.2660.3625180.35896460.65740.75766491.33

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