9GJF | pdb_00009gjf

Entamoeba histolytica Gal/GalNAc lectin in presence of monoclonal antibody CP33-H/L-LA22, mode 3

PDB DOI: https://doi.org/10.2210/pdb9GJF/pdb
EM Map EMD-51390: EMDB EMDataResource

Classification: CELL ADHESION
Organism(s): Entamoeba histolytica HM-1:IMSS
Mutation(s): No

Deposited: 2024-08-22 Released: 2026-02-11
Deposition Author(s): Gerard, S.F., Higgins, M.K.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9GJF

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for carbohydrate recognition by the Gal/GalNAc lectin of Entamoeba histolytica

Gerard, S.F., Higgins, M.K.

To be published.

Macromolecule Content

Total Structure Weight: 128.58 kDa
Atom Count: 8,671
Modeled Residue Count: 1,071
Deposited Residue Count: 1,108
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1	A [auth H]	820	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0
UniProt
Find proteins for P32022 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore P32022 Go to UniProtKB: P32022
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32022
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A [auth H]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose/N-acetyl-D-galactosamine lectin light subunit 1	B [auth L]	288	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0
UniProt
Find proteins for Q03077 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore Q03077 Go to UniProtKB: Q03077
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03077
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	3		N-Glycosylation	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth B]	7		N-Glycosylation	Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
Glycosylation Resources
GlyTouCan: G46836GH GlyCosmos: G46836GH GlyGen: G46836GH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain E [auth H]	E [auth H], F [auth H], G [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2026-02-11
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.