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- PDB-1onq: Crystal Structure of CD1a in Complex with a Sulfatide -

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Basic information

Entry
Database: PDB / ID: 1onq
TitleCrystal Structure of CD1a in Complex with a Sulfatide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • T-cell surface glycoprotein CD1a
KeywordsIMMUNE SYSTEM / Protein-Glycolipid complex / beta sheet platform
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 / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / lipopeptide binding / retina homeostasis / regulation of membrane depolarization / positive regulation of ferrous iron binding ...: / : / 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 / retina homeostasis / regulation of membrane depolarization / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response / learning or memory / endosome membrane / defense response to Gram-positive bacterium / immune response / membrane raft / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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
alpha-L-fucopyranose / Chem-SLF / Beta-2-microglobulin / T-cell surface glycoprotein CD1a / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZajonc, D.M. / Elsliger, M.A. / Teyton, L. / Wilson, I.A.
CitationJournal: Nat.Immunol. / Year: 2003
Title: Crystal structure of CD1a in complex with a sulfatide self antigen at a resolution of 2.15 A.
Authors: Zajonc, D.M. / Elsliger, M.A. / Teyton, L. / Wilson, I.A.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 CD1a
B: Beta-2-microglobulin
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,32413
Polymers88,5174
Non-polymers3,8069
Water8,107450
1
A: T-cell surface glycoprotein CD1a
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4477
Polymers44,2592
Non-polymers2,1885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-0 kcal/mol
Surface area20250 Å2
MethodPISA
2
C: T-cell surface glycoprotein CD1a
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8766
Polymers44,2592
Non-polymers1,6184
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-10 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.407, 42.711, 204.217
Angle α, β, γ (deg.)90.00, 90.78, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiologically active subunit is a heterodimer of CD1a and beta-2-microglobulin

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein T-cell surface glycoprotein CD1a / CD1a antigen / T-cell surface antigen T6/Leu-6 / hTa1 thymocyte antigen


Mass: 32510.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1A / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P06126
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / HDCMA22P


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pRMHa3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01884, UniProt: P61769*PLUS

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Sugars , 4 types, 7 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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 / N-Acetylglucosamine


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 , 2 types, 452 molecules

#6: Chemical ChemComp-SLF / SULFATE-3-D-GALACTOSYL-BETA-1-1-N-STEAROYL-D-SPHINGOSINE


Mass: 808.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H81NO11S
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 277 K / pH: 8.5
Details: MPEG 2000, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K, pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / PH range low: 8.5 / PH range high: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114 mg/mlprotein1drop
218 %PEG2000 MME1reservoir
30.1 MTris-HCl1reservoirpH8.0-8.5

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2002
RadiationMonochromator: SI 220 SINGLE CRYSTAL, CYLINDRICALLY BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 48912 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 2.15→2.19 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.44 / % possible all: 76.6
Reflection
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 40 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 76.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZQ

1gzq


Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.285 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2236 4.6 %RANDOM
Rwork0.227 ---
obs0.229 46342 92 %-
all-46342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 237 450 6791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216552
X-RAY DIFFRACTIONr_bond_other_d0.0020.025623
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9498896
X-RAY DIFFRACTIONr_angle_other_deg0.901313091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.875741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.027105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021378
X-RAY DIFFRACTIONr_nbd_refined0.190.21104
X-RAY DIFFRACTIONr_nbd_other0.2350.26410
X-RAY DIFFRACTIONr_nbtor_other0.0850.23857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5781.53722
X-RAY DIFFRACTIONr_mcangle_it1.07626007
X-RAY DIFFRACTIONr_scbond_it1.58832830
X-RAY DIFFRACTIONr_scangle_it2.5324.52889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 133
Rwork0.385 2934
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)
12.91512.03920.13954.86811.0090.4791-0.05390.1372-0.1395-0.1956-0.014-0.20190.13460.14290.06790.09780.0343-0.01470.38320.00230.244923.4152-9.090469.5036
23.63840.7103-1.25022.3062-0.58644.10550.095-0.12650.07620.17680.04020.1549-0.077-0.0701-0.13520.13590.0080.00050.1645-0.00830.21332.08168.726297.1054
32.4314-1.7106-0.13186.33631.5613.08820.04030.2214-0.0125-0.1552-0.16550.5608-0.1959-0.31310.12520.0037-0.0136-0.02890.26330.02120.2636-0.79355.375775.1587
42.6461-2.60010.30045.24730.96062.1030.0445-0.27120.130.07960.0794-0.2666-0.08170.2156-0.12390.4035-0.01780.02730.4083-0.01170.279531.90349.847740.5755
52.9431-0.52220.62492.0616-1.15566.6782-0.04970.0999-0.0403-0.27240.06260.02110.0982-0.0098-0.01290.6104-0.01340.06640.167-0.01820.256628.018-7.65976.2418
61.6140.7501-0.15936.13742.77893.7208-0.059-0.0303-0.1117-0.1725-0.19580.60330.2235-0.58980.25480.4927-0.0101-0.03320.36960.01720.282713.7752-4.799423.0957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1817 - 181
2X-RAY DIFFRACTION1AL601
3X-RAY DIFFRACTION1AE501 - 502
4X-RAY DIFFRACTION1AG511 - 512
5X-RAY DIFFRACTION1AH521 - 522
6X-RAY DIFFRACTION2AA182 - 280182 - 280
7X-RAY DIFFRACTION3BB1 - 991 - 99
8X-RAY DIFFRACTION4CC7 - 1817 - 181
9X-RAY DIFFRACTION4CM602
10X-RAY DIFFRACTION4CI501 - 502
11X-RAY DIFFRACTION4CK511
12X-RAY DIFFRACTION5CC182 - 279182 - 279
13X-RAY DIFFRACTION6DD1 - 991 - 99
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5

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