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- PDB-5c9j: Human CD1c with ligands in A' and F' channel -

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Basic information

Entry
Database: PDB / ID: 5c9j
TitleHuman CD1c with ligands in A' and F' channel
Components
  • Beta-2-microglobulin
  • T-cell surface glycoprotein CD1c,T-cell surface glycoprotein CD1b
KeywordsIMMUNE SYSTEM / Antigen Presentation / CD1 / human CD1 / MHC-like / Immunology / lipid antigen
Function / homology
Function and homology information


glycolipid binding / T cell activation involved in immune response / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding ...glycolipid binding / T cell activation involved in immune response / endogenous lipid antigen binding / exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / lysosome / endosome membrane / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / PHOSPHATE ION / STEARIC ACID / T-cell surface glycoprotein CD1b / T-cell surface glycoprotein CD1c / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTews, I. / Machelett, M.M. / Mansour, S. / Gadola, S.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
HEFCE United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells.
Authors: Mansour, S. / Tocheva, A.S. / Cave-Ayland, C. / Machelett, M.M. / Sander, B. / Lissin, N.M. / Molloy, P.E. / Baird, M.S. / Stubs, G. / Schroder, N.W. / Schumann, R.R. / Rademann, J. / ...Authors: Mansour, S. / Tocheva, A.S. / Cave-Ayland, C. / Machelett, M.M. / Sander, B. / Lissin, N.M. / Molloy, P.E. / Baird, M.S. / Stubs, G. / Schroder, N.W. / Schumann, R.R. / Rademann, J. / Postle, A.D. / Jakobsen, B.K. / Marshall, B.G. / Gosain, R. / Elkington, P.T. / Elliott, T. / Skylaris, C.K. / Essex, J.W. / Tews, I. / Gadola, S.D.
History
DepositionJun 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,46411
Polymers43,2202
Non-polymers1,2439
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-21 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.130, 97.130, 115.080
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


Mass: 31472.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1C, CD1B / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P29017, UniProt: P29016
#2: Protein Beta-2-microglobulin


Mass: 11748.161 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET23d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P61769

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Non-polymers , 5 types, 125 molecules

#3: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#4: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Magnesium chloride, 0.1M Tris pH 8, 10% PEG 8000, 1:1 protein to precipitant ratio.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.839
11-h,-k,l20.161
ReflectionResolution: 2.4→28.34 Å / Num. obs: 46442 / % possible obs: 97.8 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 3.04 % / Biso Wilson estimate: 52.941 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.066 / Χ2: 1.063 / Net I/σ(I): 15.39 / Num. measured all: 141258
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.460.6220.5991.786330346929460.75684.9
2.46-2.530.6890.5072.177417342131270.63391.4
2.53-2.60.7920.4013.069126336232980.49298.1
2.6-2.680.8460.343.9610163324932260.41199.3
2.68-2.770.9030.2724.8910144313431320.32799.9
2.77-2.870.9380.2056.269895305330490.24799.9
2.87-2.980.9610.167.999311287428730.192100
2.98-3.10.9760.12310.149189284128380.14899.9
3.1-3.240.9870.08713.868832273127280.10599.9
3.24-3.390.9920.06517.748159252925280.079100
3.39-3.580.9950.05221.567778249224600.06298.7
3.58-3.80.9960.04325.217243229122760.05199.3
3.8-4.060.9970.03628.956817219121710.04499.1
4.06-4.380.9980.03131.876484203820330.03799.8
4.38-4.80.9980.02835.075884186518580.03499.6
4.8-5.370.9980.02834.825373169816930.03499.7
5.37-6.20.9970.03132.884620147114680.03799.8
6.2-7.590.9970.03133.273863126912620.03799.4
7.59-10.730.9990.02239.4531439809790.02699.9
10.730.9990.01940.5214875244970.02394.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Coot0.8.1model building
PHASER1.8.4phasing
XSCALE03.11.14data scaling
XDS03.11.14data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OV6

3ov6


Resolution: 2.4→28.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.852 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20006 1992 8.2 %RANDOM
Rwork0.15453 ---
obs0.15823 22416 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.771 Å2
Baniso -1Baniso -2Baniso -3
1--8.85 Å20 Å20 Å2
2---8.85 Å20 Å2
3---17.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 82 116 3250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0193246
X-RAY DIFFRACTIONr_bond_other_d0.0060.022976
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9464394
X-RAY DIFFRACTIONr_angle_other_deg1.18836869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2145384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59124.025159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3381515
X-RAY DIFFRACTIONr_chiral_restr0.1470.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213654
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6085.1191524
X-RAY DIFFRACTIONr_mcbond_other4.6035.1181523
X-RAY DIFFRACTIONr_mcangle_it6.1387.6571903
X-RAY DIFFRACTIONr_mcangle_other6.1367.6581904
X-RAY DIFFRACTIONr_scbond_it5.7525.581719
X-RAY DIFFRACTIONr_scbond_other5.75.5751711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9318.1512476
X-RAY DIFFRACTIONr_long_range_B_refined9.66441.0843523
X-RAY DIFFRACTIONr_long_range_B_other9.6640.9813505
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 118 -
Rwork0.219 1369 -
obs--83.17 %
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)
10.9753-0.15811.29131.4656-0.35722.17130.01950.00680.01160.031-0.0464-0.02540.04040.01620.02680.00770.00220.00370.00860.00080.0038-5.89629.5990.463
23.07291.69-21.4151-0.90661.42590.1111-0.18550.06590.0428-0.07940.0621-0.04750.0746-0.03170.0581-0.0219-0.06040.0793-0.02520.098-38.83210.8056.213
32.65781.11310.9961.44710.41.83450.10140.0432-0.39140.03710.0874-0.11110.2568-0.0323-0.18880.04250.0038-0.03670.0243-0.02820.1037-17.5234.2722.986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 184
2X-RAY DIFFRACTION2A185 - 285
3X-RAY DIFFRACTION3B1 - 99

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