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- PDB-3he7: Crystal structure of mouse CD1d-alpha-galactosylceramide with mou... -

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Basic information

Entry
Database: PDB / ID: 3he7
TitleCrystal structure of mouse CD1d-alpha-galactosylceramide with mouse Valpha14-Vbeta7 NKT TCR
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Valpha14(mouse variable domain, human constant domain)
  • Vbeta7(mouse variable domain, human constant domain)
KeywordsIMMUNE SYSTEM / mouse CD1d / mouse NKT T-cell receptors / Cell membrane / Disulfide bond / Endosome / Glycoprotein / Immune response / Immunoglobulin domain / Innate immunity / Lysosome / Membrane / Transmembrane / MHC I
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 / alpha-beta T cell receptor complex / positive thymic T cell selection / positive regulation of macrophage activation / Endosomal/Vacuolar pathway ...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 / alpha-beta T cell receptor complex / 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 / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of interleukin-4 production / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / regulation of immune response / cellular defense response / T cell receptor binding / Neutrophil degranulation / positive regulation of interleukin-2 production / response to bacterium / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / sensory perception of smell / late endosome / Downstream TCR signaling / T cell receptor signaling pathway / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / early endosome / lysosome / endosome membrane / external side of plasma membrane / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...MHC-I family domain / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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-AGH / T cell receptor alpha chain constant / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPatel, O. / Rossjohn, J.
CitationJournal: Immunity / Year: 2009
Title: Differential recognition of CD1d-alpha-galactosyl ceramide by the V beta 8.2 and V beta 7 semi-invariant NKT T cell receptors
Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / ...Authors: Pellicci, D.G. / Patel, O. / Kjer-Nielsen, L. / Pang, S.S. / Sullivan, L.C. / Kyparissoudis, K. / Brooks, A.G. / Reid, H.H. / Gras, S. / Lucet, I.S. / Koh, R. / Smyth, M.J. / Mallevaey, T. / Matsuda, J.L. / Gapin, L. / McCluskey, J. / Godfrey, D.I. / Rossjohn, J.
History
DepositionMay 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 29, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.details / _entity.pdbx_description ..._entity.details / _entity.pdbx_description / _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.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details
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_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 2.1Nov 1, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: 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: Valpha14(mouse variable domain, human constant domain)
D: Vbeta7(mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4998
Polymers96,7744
Non-polymers1,7254
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-65 kcal/mol
Surface area39740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.229, 81.913, 243.253
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 , 3 types, 3 molecules ABD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 34662.012 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBacp10pH / 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: pBacp10pH / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01887
#4: Protein Vbeta7(mouse variable domain, human constant domain)


Mass: 27672.010 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: pET / Production host: Escherichia coli (E. coli)

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Antibody / Non-polymers , 2 types, 46 molecules C

#3: Antibody Valpha14(mouse variable domain, human constant domain)


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: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P01848*PLUS
#8: 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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Sugars , 3 types, 4 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
#7: Sugar ChemComp-AGH / N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE


Type: D-saccharide / Mass: 858.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C50H99NO9

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Details

Has protein modificationY
Sequence detailsFOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR ...FOR CHAIN C, RESIDUES 1 TO 116 IS MOUSE VARIABLE DOMAIN AND 117-210 IS HUMAN CONSTANT DOMAIN. FOR CHAIN D, RESIDUES 1 TO 117 IS MOUSE VARIABLE DOMAIN AND 118-247 IS HUMAN CONSTANT DOMAIN. THE SWISS-PROT ENTRY P11609 CONFLICTS WITH BRADBURY ET AL., 1988 WHICH SUGGESTS A HISTIDINE IN PLACE OF ASPARTATE. SEQUENCE IN THIS PDB AGREES WITH THE CITATION.

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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 Å3/Da / Density % sol: 58.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% polyethylene glycol 10K, 0.1M ammonium acetate, 0.1M Bis Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95667 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95667 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 29526 / Num. obs: 29526 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 61.2 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.707 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4192 / Rsym value: 0.707 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HE6

3he6


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.875 / SU B: 34.875 / SU ML: 0.316 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 1.46 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27117 1480 5 %RANDOM
Rwork0.22368 ---
obs0.22614 28041 99.65 %-
all-28041 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.162 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6528 0 116 45 6689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216821
X-RAY DIFFRACTIONr_angle_refined_deg1.0291.9489251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53224.211323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.983151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1851537
X-RAY DIFFRACTIONr_chiral_restr0.0650.21005
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025136
X-RAY DIFFRACTIONr_nbd_refined0.1840.22536
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24454
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.28
X-RAY DIFFRACTIONr_mcbond_it0.2291.54179
X-RAY DIFFRACTIONr_mcangle_it0.40326572
X-RAY DIFFRACTIONr_scbond_it0.54533049
X-RAY DIFFRACTIONr_scangle_it0.9144.52679
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 108 -
Rwork0.341 2011 -
obs-2119 99.2 %

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