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- PDB-5vcj: Structure of alpha-galactosylphytosphingosine bound by CD1d and i... -

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Basic information

Entry
Database: PDB / ID: 5vcj
TitleStructure of alpha-galactosylphytosphingosine bound by CD1d and in complex with the Va14Vb8.2 TCR
Components
  • (Chimeric TCR ...) x 2
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
KeywordsIMMUNE SYSTEM / antigen-presentation / TCR / MHC-fold
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 regulation of macrophage activation ...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 regulation of macrophage activation / positive thymic T cell selection / 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 / 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 / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / positive regulation of immune response / positive regulation of T cell activation / sensory perception of smell / late endosome / 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 / lysosome / early endosome / learning or memory / 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 / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : ...: / : / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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-N57 / PALMITIC ACID / T cell receptor alpha variable 11 / Human nkt tcr alpha chain / Beta-2-microglobulin / Antigen-presenting glycoprotein CD1d1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.16 Å
AuthorsWang, J. / Zajonc, D.M.
CitationJournal: Org. Biomol. Chem. / Year: 2019
Title: Enhancing T cell responses and tumour immunity by vaccination with peptides conjugated to a weak NKT cell agonist.
Authors: Compton, B.J. / Farrand, K.J. / Tang, C.W. / Osmond, T.L. / Speir, M. / Authier-Hall, A. / Wang, J. / Ferguson, P.M. / Chan, S.T.S. / Anderson, R.J. / Cooney, T.R. / Hayman, C.M. / Williams, ...Authors: Compton, B.J. / Farrand, K.J. / Tang, C.W. / Osmond, T.L. / Speir, M. / Authier-Hall, A. / Wang, J. / Ferguson, P.M. / Chan, S.T.S. / Anderson, R.J. / Cooney, T.R. / Hayman, C.M. / Williams, G.M. / Brimble, M.A. / Brooks, C.R. / Yong, L.K. / Metelitsa, L.S. / Zajonc, D.M. / Godfrey, D.I. / Gasser, O. / Weinkove, R. / Painter, G.F. / Hermans, I.F.
History
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0May 15, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 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_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_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 3.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
D: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6119
Polymers94,3764
Non-polymers2,2355
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-17 kcal/mol
Surface area37900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.261, 191.611, 151.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 1 / Fragment: Ectodomain (UNP residues 19-297) / Mutation: D201H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACp10pH / 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 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pBACp10pH / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01887

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Chimeric TCR ... , 2 types, 2 molecules CD

#3: Protein Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain) / T cell receptor alpha variable 11D / Human nkt tcr beta chain


Mass: 23055.621 Da / Num. of mol.: 1
Fragment: UNP A0A0B4J1J9 residues 22-114,UNP K7N5M3 residues 116-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav11, Trav11d, B2M, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J1J9, UniProt: K7N5M3
#4: Protein Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)


Mass: 27026.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 2 types, 3 molecules

#5: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_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]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: 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
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, 2 molecules

#6: Chemical ChemComp-N57 / (2S,3S,4R)-2-amino-3,4-dihydroxyoctadecyl alpha-D-galactopyranoside


Mass: 479.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H49NO8
#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20 % polyethylene glycol 3350, 200 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 1, 2017
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→95.82 Å / Num. obs: 19762 / % possible obs: 98.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.083 / Rrim(I) all: 0.192 / Χ2: 1.177 / Net I/σ(I): 3.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.15-3.264.20.4410.7970.2380.5050.55496.4
3.26-3.394.40.380.8310.20.4320.61896.5
3.39-3.555.10.3280.9120.1580.3660.799.6
3.55-3.735.20.2720.9260.1310.3030.63999.6
3.73-3.975.10.2320.9540.1110.2580.7799.6
3.97-4.275.10.1690.9760.0810.1880.80897.3
4.27-4.75.40.130.9890.060.1440.80499.6
4.7-5.385.20.1230.9860.0580.1360.83498.5
5.38-6.785.50.1330.9860.0610.1470.79299.2
6.78-405.10.0880.9880.0420.0984.85997.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7Y, 3QUZ

2q7y

3quz


Resolution: 3.16→95.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.874 / SU B: 21.809 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.473
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 959 4.9 %RANDOM
Rwork0.1887 ---
obs0.1916 18777 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.18 Å2 / Biso mean: 51.621 Å2 / Biso min: 31.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.29 Å2
Refinement stepCycle: final / Resolution: 3.16→95.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6361 0 150 0 6511
Biso mean--73.7 --
Num. residues----805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196691
X-RAY DIFFRACTIONr_bond_other_d0.0010.025874
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.959104
X-RAY DIFFRACTIONr_angle_other_deg0.8353.00513705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46924.272309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0131535
X-RAY DIFFRACTIONr_chiral_restr0.0680.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021361
LS refinement shellResolution: 3.159→3.241 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 77 -
Rwork0.29 1229 -
all-1306 -
obs--89.64 %

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