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Yorodumi- EMDB-34740: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34740 | |||||||||
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Title | Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Tl-gal / T-cell immunoglobulin mucin-3 / Tim3 / complex / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information 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 / toll-like receptor 7 signaling pathway / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...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 / toll-like receptor 7 signaling pathway / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of defense response to bacterium / galactoside binding / toll-like receptor 3 signaling pathway / negative regulation of immunological synapse formation / 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 / toll-like receptor 9 signaling pathway / macrophage activation involved in immune response / mediator complex / positive regulation of macrophage activation / anchoring junction / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / positive regulation of interleukin-4 production / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor 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 type II interferon production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / early endosome / defense response to Gram-positive bacterium / inflammatory response / membrane raft / innate immune response / negative regulation of gene expression / regulation of transcription by RNA polymerase II / cell surface / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Toxascaris leonina (invertebrata) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.82 Å | |||||||||
Authors | Han CW / Jang SB | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published 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 | emd_34740.map.gz | 590 KB | EMDB map data format | |
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Header (meta data) | emd-34740-v30.xml emd-34740.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34740_fsc.xml | 4.4 KB | Display | FSC data file |
Images | emd_34740.png | 13.3 KB | ||
Filedesc metadata | emd-34740.cif.gz | 5.4 KB | ||
Others | emd_34740_additional_1.map.gz emd_34740_half_map_1.map.gz emd_34740_half_map_2.map.gz | 3.6 MB 3.5 MB 3.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34740 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34740 | HTTPS FTP |
-Validation report
Summary document | emd_34740_validation.pdf.gz | 567.7 KB | Display | EMDB validaton report |
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Full document | emd_34740_full_validation.pdf.gz | 567.2 KB | Display | |
Data in XML | emd_34740_validation.xml.gz | 5.2 KB | Display | |
Data in CIF | emd_34740_validation.cif.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34740 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34740 | HTTPS FTP |
-Related structure data
Related structure data | 8hgjMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34740.map.gz / Format: CCP4 / Size: 638.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
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 |
-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: Toxascaris leonina (invertebrata) |
-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: Homo sapiens (human) |
-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: Toxascaris leonina (invertebrata) |
Molecular weight | Theoretical: 31.495289 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Homo sapiens (human) |
Molecular weight | Theoretical: 12.08181 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 200 |
Vitrification | Cryogen name: NITROGEN |
-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: FIELD EMISSION GUN |
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 |