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- PDB-8sos: Human CD1d presenting sphingomyelin C24:1 in complex with VHH nan... -

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Basic information

Entry
Database: PDB / ID: 8sos
TitleHuman CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17
Components
  • Antigen-presenting glycoprotein CD1d
  • Beta-2-microglobulin
  • Nanobody VHH ID17
KeywordsIMMUNE SYSTEM / CD1d / sphingomyelin / NKT / nanobody / VHH / 1D17
Function / homology
Function and homology information


lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen 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 / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / T cell selection / endogenous lipid antigen 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 / cell adhesion molecule binding / positive regulation of T cell proliferation / 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 / basolateral plasma membrane / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / lysosome / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm / 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
sphingomyelin / Antigen-presenting glycoprotein CD1d / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsShahine, A. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE210101031 Australia
CitationJournal: J Immunother Cancer / Year: 2023
Title: Enhanced CD1d phosphatidylserine presentation using a single-domain antibody promotes immunomodulatory CD1d-TIM-3 interactions.
Authors: Lameris, R. / Shahine, A. / Veth, M. / Westerman, B. / Godfrey, D.I. / Lutje Hulsik, D. / Brouwer, P. / Rossjohn, J. / de Gruijl, T.D. / van der Vliet, H.J.
History
DepositionApr 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
D: Nanobody VHH ID17
E: Antigen-presenting glycoprotein CD1d
F: Beta-2-microglobulin
G: Nanobody VHH ID17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,97412
Polymers130,4616
Non-polymers2,5136
Water10,305572
1
A: Antigen-presenting glycoprotein CD1d
B: Beta-2-microglobulin
D: Nanobody VHH ID17
hetero molecules

E: Antigen-presenting glycoprotein CD1d
F: Beta-2-microglobulin
G: Nanobody VHH ID17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,97412
Polymers130,4616
Non-polymers2,5136
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
Buried area10850 Å2
ΔGint-35 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.449, 136.449, 166.767
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein Antigen-presenting glycoprotein CD1d / R3G1


Mass: 39471.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1D / Plasmid: pHLSEC / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / 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 / Plasmid: pHLSEC / Cell line (production host): HEK 293S / Production host: Homo sapiens (human) / References: UniProt: P61769

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Antibody / Sugars , 2 types, 6 molecules DG

#3: Antibody Nanobody VHH ID17


Mass: 13879.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: 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.: 4 / Source method: obtained synthetically / 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 , 2 types, 574 molecules

#4: Chemical ChemComp-FO4 / sphingomyelin


Mass: 814.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H94N2O6P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 3.44 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG8000, 0.05 M zinc acetate, 0.05 M MES, pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.33→44.66 Å / Num. obs: 77042 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.998 / Rpim(I) all: 0.0286 / Net I/σ(I): 20
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7630 / CC1/2: 0.795 / Rpim(I) all: 0.359 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2PO6 & 3P0G

2po6

3p0g


Resolution: 2.33→44.66 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 3991 5.18 %
Rwork0.2093 --
obs0.2103 76985 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7801 0 168 572 8541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028212
X-RAY DIFFRACTIONf_angle_d0.47411153
X-RAY DIFFRACTIONf_dihedral_angle_d13.3422971
X-RAY DIFFRACTIONf_chiral_restr0.0411198
X-RAY DIFFRACTIONf_plane_restr0.0031411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.360.38341200.32842509X-RAY DIFFRACTION100
2.36-2.390.37821260.31712522X-RAY DIFFRACTION100
2.39-2.420.32251290.28722490X-RAY DIFFRACTION100
2.42-2.450.28221640.27042453X-RAY DIFFRACTION100
2.45-2.480.30591030.27472538X-RAY DIFFRACTION100
2.48-2.520.27661280.25742489X-RAY DIFFRACTION100
2.52-2.550.27581590.24472453X-RAY DIFFRACTION100
2.55-2.590.26441310.23272499X-RAY DIFFRACTION100
2.59-2.640.27871270.24722511X-RAY DIFFRACTION100
2.64-2.680.28331600.27592480X-RAY DIFFRACTION100
2.68-2.730.24781050.24652557X-RAY DIFFRACTION100
2.73-2.780.25891210.24122484X-RAY DIFFRACTION100
2.78-2.840.26041280.24632541X-RAY DIFFRACTION100
2.84-2.90.26791490.25082467X-RAY DIFFRACTION100
2.9-2.970.2951190.26512499X-RAY DIFFRACTION100
2.97-3.040.32161790.25362458X-RAY DIFFRACTION100
3.04-3.130.28381440.23622511X-RAY DIFFRACTION100
3.13-3.220.2181320.21042531X-RAY DIFFRACTION100
3.22-3.320.23771630.19722487X-RAY DIFFRACTION100
3.32-3.440.20441510.20392487X-RAY DIFFRACTION100
3.44-3.580.23241320.20012524X-RAY DIFFRACTION100
3.58-3.740.21051450.20072513X-RAY DIFFRACTION100
3.74-3.940.2071450.18392511X-RAY DIFFRACTION99
3.94-4.190.17691400.17292519X-RAY DIFFRACTION100
4.19-4.510.18361390.1542558X-RAY DIFFRACTION100
4.51-4.960.16331340.15052533X-RAY DIFFRACTION100
4.96-5.680.22331280.18342602X-RAY DIFFRACTION100
5.68-7.150.23381540.21572570X-RAY DIFFRACTION100
7.15-44.660.20041360.21282698X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75471.5916-0.00454.11740.54991.0586-0.07940.12450.013-0.04610.1348-0.0093-0.0039-0.0351-0.07540.3223-0.0017-0.01630.228-0.00760.228563.17262.5313-22.9787
22.7646-0.08080.83384.0105-0.53654.0935-0.1792-0.2635-0.32650.4663-0.15631.15570.2633-1.43360.22740.4557-0.12840.11430.6757-0.17120.686536.4453-19.6862-18.8201
33.4691-0.70790.49083.2457-0.62054.1716-0.0854-0.4133-0.39430.17180.14880.20460.363-0.0815-0.02310.31140.0226-0.00370.2190.04130.245253.9051-13.75-5.3228
42.10310.8732-0.632.1713-0.28331.8205-0.38890.347-0.2912-0.7310.2138-0.55380.35650.01030.17480.6232-0.13610.26250.419-0.16890.514987.396111.3993-45.5166
52.18380.14050.04092.38540.2991.3199-0.01320.00490.0866-0.1034-0.0788-0.2706-0.13710.1670.09010.2342-0.0233-0.01650.24850.0480.217171.1756-24.370315.8243
60.8690.4866-0.25320.7698-1.0921.89960.31770.88150.4201-1.3648-0.142-0.6183-0.8996-0.0894-0.12111.25830.04670.40551.09470.31360.736688.9717-13.1008-10.9531
74.02940.7859-0.6851.79360.23962.8380.04480.5236-0.2103-0.4896-0.0027-1.0177-0.00080.9270.00160.3650.01480.17260.67140.07640.695894.6082-28.12815.2329
82.765-0.0704-1.42312.50231.01324.51860.051-0.17820.29260.1862-0.11370.209-0.0455-0.00520.06910.3406-0.0377-0.02940.2536-0.08890.283552.3215-14.394542.5858
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 200 )
2X-RAY DIFFRACTION2chain 'A' and (resid 201 through 278 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 98 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 127 )
5X-RAY DIFFRACTION5chain 'E' and (resid 4 through 203 )
6X-RAY DIFFRACTION6chain 'E' and (resid 204 through 278 )
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 98 )
8X-RAY DIFFRACTION8chain 'G' and (resid 1 through 127 )

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