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- PDB-9rsf: Macaque CD1d with lipid antigen bound -

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Basic information

Entry
Database: PDB / ID: 9rsf
TitleMacaque CD1d with lipid antigen bound
Components
  • Beta-2-microglobulin
  • CD1d molecule
KeywordsIMMUNE SYSTEM / CD1d / lipopeptide / lipid antigen / iNKT
Function / homology
Function and homology information


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 T cell proliferation / cell adhesion molecule binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...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 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 / intracellular iron ion homeostasis / learning or memory / 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 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
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 / CD1d molecule / Beta-2-microglobulin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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: CD1d molecule
B: Beta-2-microglobulin
C: CD1d molecule
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,07116
Polymers90,8144
Non-polymers2,25712
Water19,2761070
1
A: CD1d molecule
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4877
Polymers45,4072
Non-polymers1,0805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-29 kcal/mol
Surface area18960 Å2
MethodPISA
2
C: CD1d molecule
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5849
Polymers45,4072
Non-polymers1,1787
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-31 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.0613, 87.0613, 232.805
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-305-

CL

21A-497-

HOH

31A-566-

HOH

41A-708-

HOH

51C-741-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein CD1d molecule


Mass: 33527.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: CD1D / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta DE3 / References: UniProt: F6TR81
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
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

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Sugars , 1 types, 2 molecules

#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

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Non-polymers , 3 types, 1080 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol 0.03 M, 0.1 M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.83→54.08 Å / Num. obs: 89434 / % possible obs: 98.22 % / Redundancy: 17.1 % / Biso Wilson estimate: 24.77 Å2 / CC1/2: 1 / CC star: 1 / Rpim(I) all: 0.013 / Rrim(I) all: 0.056 / Net I/σ(I): 32.7
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 25554 / CC1/2: 0.914 / CC star: 0.977 / Rpim(I) all: 0.179 / Rrim(I) all: 0.486 / % possible all: 84.73

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Processing

Software
NameVersionClassification
DIALS3.21data reduction
xia2data scaling
gemmi0.7.1data extraction
MOLREPphasing
Coot0.9.8.86model building
Servalcat0.4.113refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→54.076 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2171 2075 -
Rwork0.171 87274 -
obs-89349 98.12 %
Displacement parametersBiso mean: 33.15 Å2
Baniso -1Baniso -2Baniso -3
1-2.81595458 Å20 Å20 Å2
2--2.81595458 Å20 Å2
3----5.63190917 Å2
Refinement stepCycle: LAST / Resolution: 1.83→54.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6056 0 151 1070 7277
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.013765600.0119
X-RAY DIFFRACTIONs_angle_nonh_deg2.033589271.8143
X-RAY DIFFRACTIONs_dihedral_angle_1_deg7.22258015
X-RAY DIFFRACTIONs_dihedral_angle_2_deg3.03352145
X-RAY DIFFRACTIONs_dihedral_angle_3_deg12.2411215810
X-RAY DIFFRACTIONs_dihedral_angle_6_deg15.277438910
X-RAY DIFFRACTIONs_chiral_restr0.09779330.132
X-RAY DIFFRACTIONs_planes0.015394560.02
X-RAY DIFFRACTIONs_nbd0.214192710.2
X-RAY DIFFRACTIONs_nbtor0.2246109530.2
X-RAY DIFFRACTIONs_hbond_nbd0.16718930.2
X-RAY DIFFRACTIONs_symmetry_nbd0.19281430.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.1974670.2
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 (%)
1.83-1.8650.2498780.237640840.88450.8452416284.8
1.865-1.9020.26151110.210742600.89390.8522437189.51
1.902-1.9410.29361060.208843470.89310.7583445393.87
1.941-1.9830.2677780.179844640.92420.8806454297.28
1.983-2.0280.18861100.167843820.9290.9035449299.38
2.028-2.0750.20661110.16143640.93680.88634475100
2.075-2.1260.23041070.162242730.93750.88084380100
2.126-2.1810.2960.168641570.9310.89594253100
2.181-2.2410.2548990.167240390.93180.85944138100
2.241-2.3060.1928850.160639410.93670.88614026100
2.306-2.3770.23361020.162438040.9330.9042390699.95
2.377-2.4550.2014870.158937260.93530.91853813100
2.455-2.5410.2093780.159936190.93850.84573697100
2.541-2.6360.2034860.157135110.93850.90513597100
2.636-2.7440.1878860.162733280.93640.90083414100
2.744-2.8650.216850.162831980.93140.90733283100
2.865-3.0050.2012830.168131240.92740.915320799.97
3.005-3.1670.1989600.175729170.91880.86982977100
3.167-3.3580.2457770.176428040.92810.89332881100
3.358-3.5890.2077760.180226190.92840.9052695100
3.589-3.8750.2014390.165924850.93780.8918252499.96
3.875-4.2430.2254590.151822590.94310.85052318100
4.243-4.740.187520.137120750.95260.87332127100
4.74-5.4660.2303370.16518690.93940.92151906100
5.466-6.6780.2291320.211715930.91320.88091625100
6.678-9.3730.2731420.206712490.90610.85931291100
9.373-54.0760.1635130.22177830.87290.9374796100

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