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- PDB-9oht: CD1c presenting GD3 ganglioside -

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Basic information

Entry
Database: PDB / ID: 9oht
TitleCD1c presenting GD3 ganglioside
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1c/T-cell surface glycoprotein CD1b chimeric protein
KeywordsLIPID BINDING PROTEIN / CD1c / lipid mediated immunity / lipid antigen presentation / GD3 / ganglioside
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
: / : / 2-(cyclohexylazaniumyl)ethanesulfonate / MALONIC ACID / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsCao, 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 GD3 ganglioside
Authors: Cao, T.P. / 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)45,7108
Polymers43,2562
Non-polymers2,4546
Water00
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 area4500 Å2
ΔGint-25 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.496, 89.496, 158.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 31497.279 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: 11759.120 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 , 4 types, 5 molecules

#4: Chemical ChemComp-A1CB4 / (2R,3R,4E)-3-hydroxy-2-octadecanamidooctadec-4-en-1-yl 5-acetamido-3,5-dideoxy-L-glycero-beta-L-altro-non-2-ulopyranonosyl-(2->8)-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->3)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside / ganglioside GD3


Mass: 1472.744 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C70H125N3O29 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1CB5 / (2S)-2,3-dihydroxypropyl heptadecanoate


Mass: 344.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40O4
#6: Chemical ChemComp-KZF / 2-(cyclohexylazaniumyl)ethanesulfonate


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#7: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4

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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: 4.23 Å3/Da / Density % sol: 70.95 % / Description: Diamond
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.46
Details: 0.1 M CHES pH 9.46 1.05 M tri-Na citrate 0.025 M tri-glycine

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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: Mar 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.98→43.64 Å / Num. obs: 15589 / % possible obs: 100 % / Redundancy: 8.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.06 / Rrim(I) all: 0.171 / Χ2: 0.99 / Net I/σ(I): 10.8 / Num. measured all: 132394
Reflection shellResolution: 2.98→3.16 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.649 / Num. unique obs: 2467 / CC1/2: 0.533 / Rpim(I) all: 0.613 / Χ2: 0.95

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Processing

Software
NameVersionClassification
PHENIX(1.21rc1_5107: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→43.64 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 793 5.1 %
Rwork0.1868 --
obs0.1886 15540 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.98→43.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 153 0 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113229
X-RAY DIFFRACTIONf_angle_d1.3774388
X-RAY DIFFRACTIONf_dihedral_angle_d26.8431151
X-RAY DIFFRACTIONf_chiral_restr0.079473
X-RAY DIFFRACTIONf_plane_restr0.01552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.170.31111440.27562391X-RAY DIFFRACTION100
3.17-3.410.27711210.23332406X-RAY DIFFRACTION100
3.41-3.750.22851230.20742452X-RAY DIFFRACTION100
3.75-4.30.2121360.17632425X-RAY DIFFRACTION100
4.3-5.410.18271490.15722450X-RAY DIFFRACTION100
5.41-43.640.22811200.17822623X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.9604 Å / Origin y: 13.064 Å / Origin z: 7.5993 Å
111213212223313233
T0.5433 Å20.0415 Å2-0.0329 Å2-0.4237 Å2-0.065 Å2--0.385 Å2
L3.9398 °21.0866 °20.5612 °2-2.0705 °20.4941 °2--2.3219 °2
S0.1513 Å °0.0265 Å °0.1282 Å °-0.1178 Å °-0.0504 Å °-0.0213 Å °-0.0444 Å °0.0694 Å °-0.0846 Å °
Refinement TLS groupSelection details: all

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