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- EMDB-34740: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex | |||||||||
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![]() | Tl-gal / T-cell immunoglobulin mucin-3 / Tim3 / complex / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway ...regulation of tolerance induction dependent upon immune response / negative regulation of interleukin-3 production / negative regulation of granulocyte colony-stimulating factor production / negative regulation of T-helper 1 type immune response / negative regulation of myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of defense response to bacterium / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / negative regulation of immunological synapse formation / toll-like receptor 3 signaling pathway / positive regulation of interleukin-1 production / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / galactoside binding / toll-like receptor 9 signaling pathway / mediator complex / macrophage activation involved in immune response / positive regulation of macrophage activation / anchoring junction / negative regulation of interleukin-2 production / negative regulation of NF-kappaB transcription factor activity / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / negative regulation of type II interferon production / immunological synapse / maternal process involved in female pregnancy / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of chemokine production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / defense response to Gram-positive bacterium / inflammatory response / membrane raft / negative regulation of gene expression / innate immune response / regulation of transcription by RNA polymerase II / cell surface / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.82 Å | |||||||||
![]() | Han CW / Jang SB | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex Authors: Han CW / Jang SB | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 590 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 4.4 KB | Display | ![]() |
Images | ![]() | 13.3 KB | ||
Filedesc metadata | ![]() | 5.3 KB | ||
Others | ![]() ![]() ![]() | 3.6 MB 3.5 MB 3.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 601.4 KB | Display | ![]() |
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Full document | ![]() | 600.9 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hgjMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.144 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_34740_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34740_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34740_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu...
Entire | Name: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex |
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Components |
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-Supramolecule #1: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu...
Supramolecule | Name: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Molecular weight | Theoretical: 480 KDa |
-Supramolecule #2: Galectin
Supramolecule | Name: Galectin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Hepatitis A virus cellular receptor 2
Supramolecule | Name: Hepatitis A virus cellular receptor 2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Galectin
Macromolecule | Name: Galectin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 31.495289 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MATETNYPVP YRSKLTEPFE PGQTLIIKGK TAEDSVRFTI NLHNTSADFS GNDVPLHISV RFDEGKIVFN TFSKGEWGKE ERKSNPYKK GDDIDIRIRA HDSKFSISVD QKEVKEYEHR VPLSSVTHFS VDGDILITYI HWGGKYYPVP YESGLAGDGL A PGKSLLIF ...String: MATETNYPVP YRSKLTEPFE PGQTLIIKGK TAEDSVRFTI NLHNTSADFS GNDVPLHISV RFDEGKIVFN TFSKGEWGKE ERKSNPYKK GDDIDIRIRA HDSKFSISVD QKEVKEYEHR VPLSSVTHFS VDGDILITYI HWGGKYYPVP YESGLAGDGL A PGKSLLIF ATPEKKGKRF HINLLKKNGD IALHFNPRFD EKAIVRNSLI SGEWGNEERE GKNPLEKGIG CDLEFRNEEY AF QIYVDGE RFATYAHRLD PHDINGLQIG GDVEVTGIQM V UniProtKB: Galectin |
-Macromolecule #2: Hepatitis A virus cellular receptor 2
Macromolecule | Name: Hepatitis A virus cellular receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 12.08181 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: VEYRAEVGQN AYLPCFYTPA APGNLVPVCW GKGACPVFEC GNVVLRTDER DVNYWTSRYW LNGDFRKGDV SLTIENVTLA DSGIYCCRI QIPGIMNDEK FNLKLVIK UniProtKB: Hepatitis A virus cellular receptor 2 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: NITROGEN |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: -1.8 µm / Nominal defocus min: -3.0 µm |