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- PDB-2gaz: Mycobacterial lipoglycan presentation by CD1d -

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Basic information

Entry
Database: PDB / ID: 2gaz
TitleMycobacterial lipoglycan presentation by CD1d
Components
  • T-cell surface glycoprotein CD1d1
  • beta-2-microglobulin
KeywordsIMMUNE SYSTEM / mycobacteria / NKT cells / TCR / CD1 / lipid antigen presentation
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 thymic T cell selection ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell differentiation / positive regulation of NK T cell activation / NK T cell differentiation / 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 thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-4 production / antigen processing and presentation / regulation of immune response / cellular defense response / T cell receptor binding / positive regulation of interleukin-2 production / Neutrophil degranulation / 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 / 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 / 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 / positive regulation of immune response / positive regulation of type II interferon production / sensory perception of smell / late endosome / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / lysosome / early endosome / endosome membrane / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / 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
Chem-XPX / : / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsZajonc, D.M.
CitationJournal: J.Immunol. / Year: 2006
Title: Structural characterization of mycobacterial phosphatidylinositol mannoside binding to mouse CD1d.
Authors: Zajonc, D.M. / Ainge, G.D. / Painter, G.F. / Severn, W.B. / Wilson, I.A.
History
DepositionMar 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_entity_src_syn / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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_src_syn.entity_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.ptnr1_label_atom_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 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details
Remark 999SEQUENCE The residue at position 219 is a His instead of Asp in the reference Bradbury et al., ...SEQUENCE The residue at position 219 is a His instead of Asp in the reference Bradbury et al., 1988, EMBO, 7, 3081-3086. Authors sequence agrees with the reference

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1d1
B: beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7826
Polymers44,2932
Non-polymers2,4894
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-11 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.835, 110.757, 107.396
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsheterodimer formed between CD1d and beta-2microglobulin

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein T-cell surface glycoprotein CD1d1 / CD1.1 antigen


Mass: 32632.668 Da / Num. of mol.: 1 / Fragment: extracellular domain, residues 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: UniProt: P11609
#2: Protein beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 cells / References: GenBank: 55153801, UniProt: P01887*PLUS

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Sugars , 2 types, 3 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
Details: 2,6-(Di-O- -D-mannopyranosyl)-1-O-(1,2-di-O-palmitoyl-sn-glycero-3-phosphoryl)-D-myo-inositol
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, 46 molecules

#5: Chemical ChemComp-XPX / (2R)-3-[(HYDROXY{[(2R,3R,5S,6R)-3,4,5-TRIHYDROXY-2,6-BIS(ALPHA-D-MANNOPYRANOSYLOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]PROPAN E-1,2-DIYL DIHEXADECANOATE / 2,6-(DI-O-D-MANNOPYRANOSYL)-1-O-(1,2-DI-O-PALMITOYL-SN-GLYCERO-3-PHOSPHORYL)-D-MYO-INOSITOL


Mass: 1135.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C53H99O23P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% Peg 4000, 0.1M sodium citrate, 10% n-propanol, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2005
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15322 / Num. obs: 15322 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 47.4 Å2 / Rsym value: 0.143 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1505 / Rsym value: 0.548 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AKR

2akr


Resolution: 2.61→48.34 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.846 / SU B: 25.384 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.759 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28032 760 5 %RANDOM
Rwork0.21245 ---
all0.21566 14514 --
obs0.21566 14514 96.69 %-
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: 46.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.61→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 166 45 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223235
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9894404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56324.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.8915502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.711515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022384
X-RAY DIFFRACTIONr_nbd_refined0.2140.21277
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.23
X-RAY DIFFRACTIONr_mcbond_it0.7121.51891
X-RAY DIFFRACTIONr_mcangle_it1.19522978
X-RAY DIFFRACTIONr_scbond_it1.71731566
X-RAY DIFFRACTIONr_scangle_it2.7344.51426
LS refinement shellResolution: 2.611→2.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 42 -
Rwork0.269 1011 -
obs-1011 93.77 %
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)
14.01750.24540.25690.4834-0.23881.6490.1098-0.1805-0.13490.1509-0.0410.09130.081-0.0654-0.0687-0.04680.01850.014-0.11810.0401-0.12763.6268-4.364724.9264
22.0637-0.75030.10915.0773-1.92422.52720.01590.26230.2265-0.2060.00940.1176-0.19810.033-0.0253-0.1299-0.00940.0163-0.12080.0035-0.09820.833222.42482.8707
33.77531.1344-1.1591.608-0.25821.9865-0.13990.1496-0.1655-0.22020.1108-0.04010.07-0.01250.029-0.05910.0144-0.0063-0.1189-0.0044-0.149518.49491.06010.1677
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 1857 - 185
2X-RAY DIFFRACTION1AC - E501 - 524
3X-RAY DIFFRACTION1AF525
4X-RAY DIFFRACTION2AA186 - 279186 - 279
5X-RAY DIFFRACTION3BB2 - 992 - 99

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