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- PDB-9ohx: CD1c presenting endogenous lipids -

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Basic information

Entry
Database: PDB / ID: 9ohx
TitleCD1c presenting endogenous lipids
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein
KeywordsIMMUNE SYSTEM / CD1c
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / : / 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
DECANE / DODECANE / (2R)-2,3-dihydroxypropyl hexadecanoate / 2-(cyclohexylazaniumyl)ethanesulfonate / HEXADECANE / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLiao, G. / Cao, T.P. / Rossjohn, J. / Shahine, A.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE210101031 Australia
CitationJournal: To Be Published
Title: CD1c presenting endogenous lipids
Authors: Liao, G. / Rossjohn, J. / Shahine, A.
History
DepositionMay 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,58610
Polymers44,8732
Non-polymers1,7138
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Eluted as monomeric heterodimer by size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-15 kcal/mol
Surface area20070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.935, 84.661, 92.510
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 , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein


Mass: 32414.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C / Production host: Homo sapiens (human)
#2: Protein Beta-2-microglobulin


Mass: 12458.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Homo sapiens (human) / References: UniProt: P61769

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Sugars , 1 types, 1 molecules

#3: 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.: 1
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 , 6 types, 267 molecules

#4: Chemical ChemComp-KZF / 2-(cyclohexylazaniumyl)ethanesulfonate


Mass: 207.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-EKG / (2R)-2,3-dihydroxypropyl hexadecanoate


Mass: 330.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H38O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-R16 / HEXADECANE


Mass: 226.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.4
Details: 100 mM CHES, 1.05 M sodium citrate, 25 mM triglycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.68→47.87 Å / Num. obs: 50885 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.99 / Rpim(I) all: 0.022 / Net I/σ(I): 18.2
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2571 / CC1/2: 0.892 / Rpim(I) all: 0.559 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→47.87 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2589 5.1 %
Rwork0.1894 --
obs0.1908 50804 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 100 260 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063260
X-RAY DIFFRACTIONf_angle_d0.8964445
X-RAY DIFFRACTIONf_dihedral_angle_d17.3841230
X-RAY DIFFRACTIONf_chiral_restr0.057475
X-RAY DIFFRACTIONf_plane_restr0.008557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.31531540.28772641X-RAY DIFFRACTION100
1.71-1.750.27941560.24712648X-RAY DIFFRACTION100
1.75-1.790.2561510.22172602X-RAY DIFFRACTION100
1.79-1.830.24221250.21682653X-RAY DIFFRACTION100
1.83-1.870.25211390.20762658X-RAY DIFFRACTION100
1.87-1.920.26711640.21342622X-RAY DIFFRACTION100
1.92-1.980.26461430.21452624X-RAY DIFFRACTION100
1.98-2.040.26531520.20892663X-RAY DIFFRACTION100
2.04-2.120.25271250.19182669X-RAY DIFFRACTION100
2.12-2.20.24261150.19382697X-RAY DIFFRACTION100
2.2-2.30.24421350.19812682X-RAY DIFFRACTION100
2.3-2.420.2171630.19352652X-RAY DIFFRACTION100
2.42-2.570.24611380.21092682X-RAY DIFFRACTION100
2.57-2.770.27151660.21482640X-RAY DIFFRACTION100
2.77-3.050.2151350.20852722X-RAY DIFFRACTION100
3.05-3.490.20471470.17842719X-RAY DIFFRACTION100
3.49-4.40.15191260.15152769X-RAY DIFFRACTION100
4.4-100.19151550.17722872X-RAY DIFFRACTION100

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