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- PDB-5l2k: Crystal structure of GEM42 TCR-CD1b-GMM complex -

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Basic information

Entry
Database: PDB / ID: 5l2k
TitleCrystal structure of GEM42 TCR-CD1b-GMM complex
Components
  • Beta-2-microglobulin
  • GEM42 TCR alpha chain
  • GEM42 TCR beta chain
  • T-cell surface glycoprotein CD1b
KeywordsIMMUNE SYSTEM / CD1b / lipid / TB / MTb / GMM / tuberculosis / GEM T cell / TCR / T cell / GEM42
Function / homology
Function and homology information


exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport ...exogenous lipid antigen binding / antigen processing and presentation, endogenous lipid antigen via MHC class Ib / lipopeptide binding / endogenous lipid antigen binding / antigen processing and presentation, exogenous lipid antigen via MHC class Ib / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endosome membrane / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / 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 / Chem-70E / : / T-cell surface glycoprotein CD1b / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsGras, S. / Shahine, A. / Le Nours, J. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2016
Title: T cell receptor recognition of CD1b presenting a mycobacterial glycolipid.
Authors: Gras, S. / Van Rhijn, I. / Shahine, A. / Cheng, T.Y. / Bhati, M. / Tan, L.L. / Halim, H. / Tuttle, K.D. / Gapin, L. / Le Nours, J. / Moody, D.B. / Rossjohn, J.
History
DepositionAug 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Other
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 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 1.4Oct 9, 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

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
D: GEM42 TCR alpha chain
E: GEM42 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,83721
Polymers95,0644
Non-polymers2,77317
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint-207 kcal/mol
Surface area37230 Å2
2
A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
E: GEM42 TCR beta chain
hetero molecules

A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
E: GEM42 TCR beta chain
hetero molecules

A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
E: GEM42 TCR beta chain
hetero molecules

A: T-cell surface glycoprotein CD1b
B: Beta-2-microglobulin
E: GEM42 TCR beta chain
hetero molecules

D: GEM42 TCR alpha chain
hetero molecules

D: GEM42 TCR alpha chain
hetero molecules

D: GEM42 TCR alpha chain
hetero molecules

D: GEM42 TCR alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,34884
Polymers380,25716
Non-polymers11,09168
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
crystal symmetry operation3_544-x+y,-x-1,z-1/31
crystal symmetry operation6_554x-y,x,z-1/31
crystal symmetry operation8_545x-y,-y-1,-z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area43120 Å2
ΔGint-733 kcal/mol
Surface area158670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.998, 174.998, 170.869
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein T-cell surface glycoprotein CD1b


Mass: 33488.609 Da / Num. of mol.: 1 / Mutation: I160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD1B / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P29016
#2: Protein Beta-2-microglobulin


Mass: 11616.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P61769
#3: Protein GEM42 TCR alpha chain


Mass: 22646.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein GEM42 TCR beta chain


Mass: 27312.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Sugars , 1 types, 3 molecules

#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.: 3
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 , 7 types, 20 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-6UL / TETRACOSYL PALMITATE


Mass: 593.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80O2
#10: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs
#11: Chemical ChemComp-70E / 6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose / C36 GLUCOSE MONOMYCOLATE / C36 GMM


Mass: 715.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82O8
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsLigand 70E, C36 GLUCOSE MONOMYCOLATE, was built with R chirality at C5, as it best fits the density ...Ligand 70E, C36 GLUCOSE MONOMYCOLATE, was built with R chirality at C5, as it best fits the density in this configuration

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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: 4.09 Å3/Da / Density % sol: 69.93 % / Mosaicity: 0.16 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5-2M NH4SO4, 0.1M Tris-HCl pH8.5, 10mM MgCl2, 10mM CeCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.2→47.73 Å / Biso Wilson estimate: 78.5 Å2
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 61.1 % / Rmerge(I) obs: 7.76 / Num. measured all: 227748 / Num. unique all: 3727 / CC1/2: 0.638 / Rpim(I) all: 0.011 / Rrim(I) all: 0.083 / Rsym value: 0.082 / Net I/σ(I) obs: 1.8 / Rejects: 0 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
SCALA3.3.21data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2J, 4G8F

5l2j

4g8f


Resolution: 3.2→47.73 Å / Cor.coef. Fo:Fc: 0.9075 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 8.754 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.376 / SU Rfree Cruickshank DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1259 4.84 %RANDOM
Rwork0.218 ---
obs0.219 26029 99.97 %-
Displacement parametersBiso mean: 80.56 Å2
Baniso -1Baniso -2Baniso -3
1--2.7014 Å20 Å20 Å2
2---2.7014 Å20 Å2
3---5.4028 Å2
Refine analyzeLuzzati coordinate error obs: 0.704 Å
Refinement stepCycle: LAST / Resolution: 3.2→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 150 6 6497
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.929025HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3002SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes957HARMONIC5
X-RAY DIFFRACTIONt_it6656HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.04
X-RAY DIFFRACTIONt_other_torsion3.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion834SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6924SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.33 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2938 134 4.66 %
Rwork0.2535 2739 -
all0.2553 2873 -
obs--99.97 %

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