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- EMDB-34740: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu... -

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Basic information

Entry
Database: EMDB / ID: EMD-34740
TitleToxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
Map data
Sample
  • Complex: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
    • Complex: Galectin
      • Protein or peptide: Galectin
    • Complex: Hepatitis A virus cellular receptor 2
      • Protein or peptide: Hepatitis A virus cellular receptor 2
KeywordsTl-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 myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction ...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 myeloid dendritic cell activation / Interleukin-2 family signaling / negative regulation of interferon-alpha production / negative regulation of T-helper 1 type immune response / negative regulation of defense response to bacterium / toll-like receptor 7 signaling pathway / natural killer cell tolerance induction / negative regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of defense response to bacterium / galactoside binding / negative regulation of immunological synapse formation / toll-like receptor 3 signaling pathway / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / positive regulation of interleukin-1 production / toll-like receptor 9 signaling pathway / mediator complex / positive regulation of macrophage activation / macrophage activation involved in immune response / 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 type II interferon production / negative regulation of interleukin-6 production / immunological synapse / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of chemokine production / negative regulation of T cell proliferation / positive regulation of T cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / early endosome / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / 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
: / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype ...: / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Galectin / Hepatitis A virus cellular receptor 2
Similarity search - Component
Biological speciesToxascaris leonina (invertebrata) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.82 Å
AuthorsHan CW / Jang SB
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
Authors: Han CW / Jang SB
History
DepositionNov 14, 2022-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_34740.png

Downloads & links

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Map

FileDownload / File: emd_34740.map.gz / Format: CCP4 / Size: 638.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.14 Å/pix.
x 39 pix.
= 44.616 Å		1.14 Å/pix.
x 59 pix.
= 67.496 Å		1.14 Å/pix.
x 71 pix.
= 81.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.144 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.23
Minimum - Maximum-9.020200000000001 - 7.463511
Average (Standard dev.)0.8041014 (±2.0210288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-22-37-18
Dimensions597139
Spacing395971
CellA: 44.616 Å / B: 67.496 Å / C: 81.22401 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_34740_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34740_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34740_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu...

EntireName: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
Components
  • Complex: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
    • Complex: Galectin
      • Protein or peptide: Galectin
    • Complex: Hepatitis A virus cellular receptor 2
      • Protein or peptide: Hepatitis A virus cellular receptor 2

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Supramolecule #1: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu...

SupramoleculeName: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 480 KDa

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Supramolecule #2: Galectin

SupramoleculeName: Galectin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Toxascaris leonina (invertebrata)

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Supramolecule #3: Hepatitis A virus cellular receptor 2

SupramoleculeName: Hepatitis A virus cellular receptor 2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Galectin

MacromoleculeName: Galectin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Toxascaris leonina (invertebrata)
Molecular weightTheoretical: 31.495289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Hepatitis A virus cellular receptor 2

MacromoleculeName: Hepatitis A virus cellular receptor 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.08181 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VEYRAEVGQN AYLPCFYTPA APGNLVPVCW GKGACPVFEC GNVVLRTDER DVNYWTSRYW LNGDFRKGDV SLTIENVTLA DSGIYCCRI QIPGIMNDEK FNLKLVIK

UniProtKB: Hepatitis A virus cellular receptor 2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 39.99 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5glv


Details: Tl-gal
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 946426
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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