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- PDB-9ged: Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 -

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Basic information

Entry
Database: PDB / ID: 9ged
TitleEntamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992
ComponentsGalactose/N-acetyl-D-galactosamine lectin heavy subunit 1
KeywordsCELL ADHESION / Entamoeba histolytica / lectin / Gal/GalNAc / trogocytosis
Function / homologycarbohydrate binding / cell adhesion / plasma membrane / Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
Function and homology information
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.484 Å
AuthorsGerard, S.F. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural basis for carbohydrate recognition by the Gal/GalNAc lectin of Entamoeba histolytica involved in host cell adhesion.
Authors: Samuel F Gérard / Christina Redfield / Matthew K Higgins /
Abstract: 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 ...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.
History
DepositionAug 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
B: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9706
Polymers65,3063
Non-polymers6643
Water1,17165
1
A: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9902
Polymers21,7691
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.138, 145.081, 85.939
Angle α, β, γ (deg.)90.000, 114.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1 / Gal/GalNAc lectin heavy subunit 1 / Galactose-inhibitable lectin 170 kDa subunit / N-acetyl D- ...Gal/GalNAc lectin heavy subunit 1 / Galactose-inhibitable lectin 170 kDa subunit / N-acetyl D-galactosamine-specific lectin


Mass: 21768.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: hgl1, EHI_133900 / Production host: Homo sapiens (human) / References: UniProt: P32022
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Sodium acetate, pH 4.0, 0.225 M Ammonium sulfate, 12 % w/v PEG 4000 + 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.48→45.34 Å / Num. obs: 20410 / % possible obs: 91.7 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rpim(I) all: 0.095 / Net I/σ(I): 5.6
Reflection shellResolution: 2.48→2.75 Å / Num. unique obs: 1020 / CC1/2: 0.524 / Rpim(I) all: 0.586

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (26-JUL-2023)refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9GEI

9gei


Resolution: 2.484→34.47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.827 / SU Rfree Blow DPI: 0.342 / SU Rfree Cruickshank DPI: 0.352
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 995 4.88 %RANDOM
Rwork0.236 ---
obs0.2371 20399 62.4 %-
Displacement parametersBiso max: 108 Å2 / Biso mean: 53.85 Å2 / Biso min: 18.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.131 Å20 Å20.2993 Å2
2--1.9252 Å20 Å2
3----2.0561 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.484→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 42 65 4505
Biso mean--46.22 34.98 -
Num. residues----544
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1651SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes771HARMONIC5
X-RAY DIFFRACTIONt_it4540HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3193SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4540HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg6139HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.6
X-RAY DIFFRACTIONt_other_torsion17.74
LS refinement shellResolution: 2.484→2.67 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3355 18 4.32 %
Rwork0.2904 399 -
obs--6.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
19.62542.23120.79621.02790.1114-0.1860.144-0.25320.50290.0684-0.07390.1437-0.0455-0.0831-0.0701-0.13220.02820.03550.0103-0.0418-0.114645.807234.603116.7588
24.7304-3.34330.44213.2049-0.5851-0.2794-0.0715-0.21960.14650.20850.1773-0.12510.03730.012-0.1058-0.02070.065-0.0749-0.0684-0.0724-0.087422.810811.925618.3916
31.16061.4572-0.3554.402-0.4229-0.2041-0.0230.0631-0.05670.17020.1704-0.19180.0089-0.061-0.1474-0.01480.0016-0.0647-0.11060.0075-0.041854.54113.928423.0146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ C|808 - C|992 }C808 - 992
2X-RAY DIFFRACTION2{ A|808 - A|992 }A808 - 992
3X-RAY DIFFRACTION3{ B|808 - B|992 }B808 - 992

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