[English] 日本語
Yorodumi
- PDB-8hgj: Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hgj
TitleToxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complex
Components
  • Galectin
  • Hepatitis A virus cellular receptor 2
KeywordsIMMUNE SYSTEM / Tl-gal / T-cell immunoglobulin mucin-3 / Tim3 / complex
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 / 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 / macrophage activation involved in immune response / 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 chemokine production / 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 / 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
: / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.82 Å
AuthorsHan, C.W. / Jang, S.B.
Funding support1items
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, C.W. / Jang, S.B.
History
DepositionNov 14, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galectin
B: Hepatitis A virus cellular receptor 2


Theoretical massNumber of molelcules
Total (without water)43,5772
Polymers43,5772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein Galectin


Mass: 31495.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxascaris leonina (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L1QJZ7
#2: Protein Hepatitis A virus cellular receptor 2 / HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell ...HAVcr-2 / T-cell immunoglobulin and mucin domain-containing protein 3 / TIMD-3 / T-cell immunoglobulin mucin receptor 3 / TIM-3 / T-cell membrane protein 3


Mass: 12081.810 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAVCR2, TIM3, TIMD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDQ0
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Toxascaris leonina galectin (Tl-gal) and Human T-cell immunoglobulin mucin-3 (Tim3) complexCOMPLEXall0RECOMBINANT
2GalectinCOMPLEX#11RECOMBINANT
3Hepatitis A virus cellular receptor 2COMPLEX#21RECOMBINANT
Molecular weightValue: 0.48 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
12Toxascaris leonina (invertebrata)59264
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: NITROGEN

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: DARK FIELD / Nominal defocus max: -1800 nm / Nominal defocus min: -3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 39.99 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.14_3260refinement
PHENIX1.14_3260refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 946426 / Symmetry type: POINT
RefinementStereochemistry target values: CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01333153
ELECTRON MICROSCOPYf_angle_d1.65824271
ELECTRON MICROSCOPYf_chiral_restr0.0672449
ELECTRON MICROSCOPYf_plane_restr0.0084561
ELECTRON MICROSCOPYf_dihedral_angle_d9.72281868

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more