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- PDB-3qi9: Crystal structure of mouse CD1d-alpha-phosphotidylinositol with m... -

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Basic information

Entry
Database: PDB / ID: 3qi9
TitleCrystal structure of mouse CD1d-alpha-phosphotidylinositol with mouse Valpha14-Vbeta6 2A3-D NKT TCR
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • NKT TCR V alpha 14
  • NKT TCR V beta 6 2A3-D
KeywordsIMMUNE SYSTEM / autoreactivity / T-cell surface
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
Chem-PII / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsClarke, A.J. / Rossjohn, J.
CitationJournal: Immunity / Year: 2011
Title: A molecular basis for NKT cell recognition of CD1d-self-antigen
Authors: Mallevaey, T. / Clarke, A.J. / Scott-Browne, J.P. / Young, M.H. / Roisman, L.C. / Pellicci, D.G. / Patel, O. / Vivian, J.P. / Matsuda, J.L. / McCluskey, J. / Godfrey, D.I. / Marrack, P. / ...Authors: Mallevaey, T. / Clarke, A.J. / Scott-Browne, J.P. / Young, M.H. / Roisman, L.C. / Pellicci, D.G. / Patel, O. / Vivian, J.P. / Matsuda, J.L. / McCluskey, J. / Godfrey, D.I. / Marrack, P. / Rossjohn, J. / Gapin, L.
History
DepositionJan 26, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms ...entity_src_gen / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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_nonpoly_scheme / pdbx_struct_assembly_gen / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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_seq_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 2.1Nov 1, 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 2.2Nov 20, 2024Group: Structure summary
Category: pdbx_contact_author / 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 CD1d1
B: Beta-2-microglobulin
C: NKT TCR V alpha 14
D: NKT TCR V beta 6 2A3-D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,32411
Polymers96,4244
Non-polymers1,9007
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13120 Å2
ΔGint-65 kcal/mol
Surface area39390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.697, 95.697, 289.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: residues in UNP 19-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pFastBac Dual / Cell line (production host): Hi 5 / Production host: Trichoplusia ni (cabbage looper) / 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: pFastBac Dual / Cell line (production host): Hi 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#3: Protein NKT TCR V alpha 14


Mass: 22779.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL
#4: Protein NKT TCR V beta 6 2A3-D


Mass: 27322.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera of Mouse variable domain and human constant domain
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL

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Sugars , 2 types, 3 molecules

#5: 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.: 1
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
#6: 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, 184 molecules

#7: Chemical ChemComp-PII / 2-[(HYDROXY{[(2R,3R,5S,6R)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL]OXY}PHOSPHORYL)OXY]-1-[(PALMITOYLOXY)METHYL]ETHYL HEPTADECANOATE


Mass: 825.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H81O13P
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsHIS A 201 IS FROM GENBANK DATABASE, BAB22206. ALA B 85 IS NATURAL VARIANT.

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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: 64.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, Sodium Citrate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.47 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 2.3→41 Å / Num. obs: 69852 / Redundancy: 13.3 % / Net I/σ(I): 15.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE7

3he7


Resolution: 2.3→39.31 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0 / SU B: 7.969 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2749 3082 5.1 %RANDOM
Rwork0.247 57767 --
obs0.2484 60849 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.15 Å2 / Biso mean: 54.3635 Å2 / Biso min: 24.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 125 180 6863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026827
X-RAY DIFFRACTIONr_angle_refined_deg0.9761.9439264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1175819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63124.548310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.146151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4151529
X-RAY DIFFRACTIONr_chiral_restr0.0610.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215155
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 194 -
Rwork0.329 3819 -
all-4013 -
obs--100 %

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