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- PDB-4zak: Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex -

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Basic information

Entry
Database: PDB / ID: 4zak
TitleCrystal structure of the mCD1d/DB06-1/iNKTCR ternary complex
Components
  • Antigen-presenting glycoprotein CD1d1
  • Beta-2-microglobulin
  • Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain
  • T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region
KeywordsIMMUNE SYSTEM / MHC-fold / Ig-fold / glycolipid antigen presentation / T cell receptor
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 / T cell receptor complex / antigen processing and presentation / positive regulation of interleukin-4 production / alpha-beta T cell activation / 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 / T cell receptor signaling pathway / negative regulation of neuron projection development / protein refolding / protein homotetramerization / adaptive immune response / 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 / membrane / 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 / Immunoglobulin V-Type ...: / : / : / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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-4LX / T cell receptor beta, constant 2 / T cell receptor alpha variable 11 / T cell receptor beta constant 2 / Possible J 18 gene segment / Beta-chain / 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: 2.824 Å
AuthorsZajonc, D.M. / Birkholz, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI074952 United States
CitationJournal: J Immunol. / Year: 2015
Title: A Novel Glycolipid Antigen for NKT Cells That Preferentially Induces IFN-gamma Production.
Authors: Birkholz, A.M. / Girardi, E. / Wingender, G. / Khurana, A. / Wang, J. / Zhao, M. / Zahner, S. / Illarionov, P.A. / Wen, X. / Li, M. / Yuan, W. / Porcelli, S.A. / Besra, G.S. / Zajonc, D.M. / Kronenberg, M.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 2.1Sep 27, 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 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain
D: T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1178
Polymers94,3764
Non-polymers1,7414
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9190 Å2
ΔGint-31 kcal/mol
Surface area36940 Å2
Unit cell
Length a, b, c (Å)78.921, 190.544, 150.760
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 , 4 types, 4 molecules ABCD

#1: Protein Antigen-presenting glycoprotein CD1d1


Mass: 32632.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd1d1, Cd1.1 / Plasmid: pBACpHp10 / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / 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 / Details (production host): dual promotor / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01887
#3: Protein Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain / Protein Trav11d / Human nkt tcr beta chain


Mass: 23055.621 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)
Gene: Trav11, Trav11d, Tcr-alpha, B2M, HDCMA22P / Plasmid: pET22b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), BL21DE3
References: UniProt: A0A0B4J1J9, UniProt: A0N4Z0, UniProt: K7N5M3
#4: Protein T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region


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+ / Gene: Trbc2, TRBC2, TCRBC2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A075B5J4, UniProt: A0A5B9, UniProt: A2NTY6*PLUS

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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 , 1 types, 1 molecules

#7: Chemical ChemComp-4LX / N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexacosanethioamide


Mass: 874.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C50H99NO8S

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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: 3 Å3/Da / Density % sol: 59.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 4000, 0.2M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2014
RadiationMonochromator: I-beam single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.824→150.76 Å / Num. all: 27210 / Num. obs: 27210 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rsym value: 0.0122 / Net I/σ(I): 10.4
Reflection shellResolution: 2.824→2.93 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.82 Å47.64 Å
Translation2.82 Å47.64 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0104refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASER2.3.0phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7Y

2q7y


Resolution: 2.824→45.42 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.875 / SU B: 13.387 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.318 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1366 5 %RANDOM
Rwork0.2159 ---
obs0.2179 25824 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.69 Å2 / Biso mean: 48.531 Å2 / Biso min: 30.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20 Å2
2--0.44 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: final / Resolution: 2.824→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 116 0 6341
Biso mean--47.95 --
Num. residues----807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226520
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9488897
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8625802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44524.286287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67215953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9311529
X-RAY DIFFRACTIONr_chiral_restr0.0550.2985
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214995
LS refinement shellResolution: 2.824→2.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 102 -
Rwork0.336 1756 -
all-1858 -
obs--97.28 %

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