[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis for carbohydrate recognition by the Gal/GalNAc lectin of Entamoeba histolytica involved in host cell adhesion.
Journal, issue, pagesPLoS Pathog, Vol. 22, Issue 2, Page e1013948, Year 2026
Publish dateFeb 24, 2026
AuthorsSamuel F Gérard / Christina Redfield / Matthew K Higgins /
PubMed AbstractIntestinal amoebiasis is caused by Entamoeba histolytica, one of the deadliest human-infective parasites. Central to its pathogenicity is its binding to mucosal carbohydrates, which precedes tissue ...Intestinal amoebiasis is caused by Entamoeba histolytica, one of the deadliest human-infective parasites. Central to its pathogenicity is its binding to mucosal carbohydrates, which precedes tissue damage by trogocytosis. Carbohydrate binding is mediated by a single adhesin, the galactose/N-acetylgalactosamine (Gal/GalNAc) lectin, which is the leading vaccine candidate for amoebiasis. We present the structure of the native heterodimeric lectin, revealing an ordered core containing the light chain and the N-terminal region of the heavy chain. Structures obtained in the presence of ligand show that the Gal/GalNAc binding site is in the light chain, which adopts a β-trefoil fold found in other lectins. An elongated arm emerges from the heavy chain, which adopts multiple positions and may be modulated by sugar binding. This study reveals the molecular basis for sugar binding by the Entamoeba histolytica Gal/GalNAc lectin, a prerequisite for parasite invasion and development of intestinal disease.
External linksPLoS Pathog / PubMed:41734235 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.818 - 3.9 Å
Structure data

EMDB-51385, PDB-9gja:
Entamoeba histolytica Gal/GalNAc lectin, mode 1
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-51386, PDB-9gjb:
Entamoeba histolytica Gal/GalNAc lectin, mode 2
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-51387, PDB-9gjc:
Entamoeba histolytica Gal/GalNAc lectin, mode 3
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-51392, PDB-9gjh:
Entamoeba histolytica Gal/GalNAc lectin bound to galactose, mode 1
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-51393, PDB-9gji:
Entamoeba histolytica Gal/GalNAc lectin bound to galactose, mode 2
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-51394, PDB-9gjj:
Entamoeba histolytica Gal/GalNAc lectin bound to galactose, mode 3
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-51395, PDB-9gjk:
Entamoeba histolytica Gal/GalNAc lectin bound to LacNAc, mode 1
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-51396, PDB-9gjl:
Entamoeba histolytica Gal/GalNAc lectin bound to LacNAc, mode 2
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-51397, PDB-9gjm:
Entamoeba histolytica Gal/GalNAc lectin bound to LacNAc, mode 3
Method: EM (single particle) / Resolution: 3.9 Å

PDB-9ged:
Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992
Method: X-RAY DIFFRACTION / Resolution: 2.484 Å

PDB-9gee:
Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of galactose
Method: X-RAY DIFFRACTION / Resolution: 1.818 Å

PDB-9geg:
Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of GalNAc
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

PDB-9geh:
Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of LacNAc
Method: X-RAY DIFFRACTION / Resolution: 2.319 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-HOH:
WATER

ChemComp-GAL:
beta-D-galactopyranose

Source
  • entamoeba histolytica hm-1:imss (eukaryote)
  • entamoeba histolytica (eukaryote)
KeywordsCELL ADHESION / Entamoeba histolytica / lectin / Gal/GalNAc / trogocytosis

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more