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- PDB-5fkp: Crystal structure of the mouse CD1d in complex with the p99 peptide -

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Basic information

Entry
Database: PDB / ID: 5fkp
TitleCrystal structure of the mouse CD1d in complex with the p99 peptide
Components
  • ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
  • BETA 2 MICROGLOBULIN
  • P99
KeywordsIMMUNE SYSTEM / CD1D / ANTIGEN PRESENTATION / ALPHA-HELICAL
Function / homology
Function and homology information


regulation of immature T cell proliferation in thymus / positive regulation of NK T cell activation / positive regulation of NK T cell differentiation / NK T cell differentiation / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway / DAP12 interactions ...regulation of immature T cell proliferation in thymus / positive regulation of NK T cell activation / positive regulation of NK T cell differentiation / NK T cell differentiation / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / 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 / antigen processing and presentation / positive regulation of interleukin-4 production / regulation of immune response / cellular defense response / T cell receptor binding / Neutrophil degranulation / positive regulation of interleukin-2 production / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / positive regulation of type II interferon production / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / late endosome / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / early endosome / lysosome / endosome membrane / lysosomal membrane / innate immune response / external side of plasma membrane / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TETRACOSYL PALMITATE / D(-)-TARTARIC ACID / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGirardi, E. / Wang, J. / Zajonc, D.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure of an Alpha-Helical Peptide and Lipopeptide Bound to the Non-Classical Mhc Class I Molecule Cd1D
Authors: Girardi, E. / Wang, J. / Zajonc, D.M.
History
DepositionOct 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Jun 1, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
B: BETA 2 MICROGLOBULIN
C: P99
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,59212
Polymers47,1433
Non-polymers2,4499
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-35.1 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.170, 107.570, 110.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1 / CD1D.1


Mass: 32609.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / 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) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide P99


Mass: 2873.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: N-TERMINAL BIOTIN / Source: (synth.) MUS MUSCULUS (house mouse)

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Sugars , 2 types, 3 molecules

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


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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.: 2
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, 278 molecules

#6: Chemical ChemComp-6UL / TETRACOSYL PALMITATE


Mass: 593.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80O2
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growDetails: 0.2M AMMONIUM TARTRATE AND 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→55 Å / Num. obs: 47272 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3G08

3g08


Resolution: 1.8→49.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.39 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23361 2374 5 %RANDOM
Rwork0.20538 ---
obs0.20681 44833 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.8→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 154 272 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193313
X-RAY DIFFRACTIONr_bond_other_d0.0020.022958
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9494516
X-RAY DIFFRACTIONr_angle_other_deg0.8993.0086800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8715387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40823.767146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7715462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4781514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213665
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02803
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_it0.5281.7861551
X-RAY DIFFRACTIONr_mcbond_other0.5281.7851550
X-RAY DIFFRACTIONr_mcangle_it0.9282.6691937
X-RAY DIFFRACTIONr_mcangle_other0.9272.671938
X-RAY DIFFRACTIONr_scbond_it0.5661.9451762
X-RAY DIFFRACTIONr_scbond_other0.5531.9381759
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9052.8592578
X-RAY DIFFRACTIONr_long_range_B_refined6.04216.0483743
X-RAY DIFFRACTIONr_long_range_B_other6.04415.9893739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 181 -
Rwork0.311 3260 -
obs--98.99 %
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)
14.5509-0.72760.54131.9188-0.68020.2940.1536-0.387-0.54570.0458-0.06740.1310.09920.0019-0.08620.3246-0.0012-0.03460.06960.09210.160128.03922.255533.3455
23.03180.3548-0.41172.4527-1.94084.8190.06220.37170.0552-0.1013-0.05570.00850.01730.1203-0.00650.02820.0124-0.00550.05250.00610.00319.987122.37315.9278
34.9208-1.38321.19111.7649-0.16042.0208-0.1744-0.3560.38930.18730.0119-0.0749-0.2382-0.0650.16250.1262-0.01120.00080.0339-0.02940.050713.240527.420326.7413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1A1280 - 1286
3X-RAY DIFFRACTION1C0 - 17
4X-RAY DIFFRACTION1A1287
5X-RAY DIFFRACTION2A181 - 280
6X-RAY DIFFRACTION3B1 - 99

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