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- EMDB-51397: Entamoeba histolytica Gal/GalNAc lectin bound to LacNAc, mode 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-51397
TitleEntamoeba histolytica Gal/GalNAc lectin bound to LacNAc, mode 3
Map data
Sample
  • Complex: Entamoeba histolytica Gal/GalNAc lectin heavy and light chains
    • Protein or peptide: Galactose/N-acetyl-D-galactosamine lectin light subunit 1
  • Protein or peptide: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEntamoeba histolytica / lectin / Gal/GalNAc / trogocytosis / CELL ADHESION
Function / homologyGalactose-inhibitable lectin 35kDa subunit / Galactose-inhibitable lectin 35 kDa subunit / carbohydrate binding / cell adhesion / plasma membrane / Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1 / Galactose/N-acetyl-D-galactosamine lectin light subunit 1
Function and homology information
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGerard SF / Higgins MK
Funding support United Kingdom, 1 items
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 22, 2024-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51397.png

Downloads & links

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Map

FileDownload / File: emd_51397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å		0.83 Å/pix.
x 256 pix.
= 212.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.2673721 - 1.9325064
Average (Standard dev.)0.0019026287 (±0.0475944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51397_msk_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_51397_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51397_half_map_2.map
Projections & Slices
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Sample components

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Entire : Entamoeba histolytica Gal/GalNAc lectin heavy and light chains

EntireName: Entamoeba histolytica Gal/GalNAc lectin heavy and light chains
Components
  • Complex: Entamoeba histolytica Gal/GalNAc lectin heavy and light chains
    • Protein or peptide: Galactose/N-acetyl-D-galactosamine lectin light subunit 1
  • Protein or peptide: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Entamoeba histolytica Gal/GalNAc lectin heavy and light chains

SupramoleculeName: Entamoeba histolytica Gal/GalNAc lectin heavy and light chains
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)

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Macromolecule #1: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1

MacromoleculeName: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 92.455273 KDa
SequenceString: MKLLLLNILL LCCLADKLNE FSADIDYYDL GIMSRGKNAG SWYHSYEHQY DVFYYLAMQP WRHFVWTTCT TTDGNKECYK YTINEDHNV KVEDINKTDI KQDFCQKEYA YPIEKYEVDW DNVPVDEQRI ESVDINGKTC FKYAAKRPLA YVYLNTKMTY A TKTEAYDV ...String:
MKLLLLNILL LCCLADKLNE FSADIDYYDL GIMSRGKNAG SWYHSYEHQY DVFYYLAMQP WRHFVWTTCT TTDGNKECYK YTINEDHNV KVEDINKTDI KQDFCQKEYA YPIEKYEVDW DNVPVDEQRI ESVDINGKTC FKYAAKRPLA YVYLNTKMTY A TKTEAYDV CRMDFIGGRS ITFRSFNTEN KAFIDQYNTN TTSKCLLKVY DNNVNTHLAI IFGITDSTVI KSLQENLSLL SQ LKTVKGV TLYYLKDDTY FTVNITLDQL KYDTLVKYTA GTGQVDPLIN IAKNDLATKV ADKSKDKNAN DKIKRGTMIV LMD TALGSE FNAETEFDRK NISVHTVVLN RNKDPKITRS ALRLVSLGPH YHEFTGNDEV NATITALFKG IRANLTERCD RDKC SGFCD AMNRCTCPMC CENDCFYTSC DVETGSCIPW PKAKPKAKKE CPATCVGSYE CKDLEGCVVT KYNDTCQPKV KCMVP YCDN DKNLTEVCKQ KANCEADQKP SSDGYCWSYT CDQTTGFCKK DKRGKEMCTG KTNNCQEYVC DSEQRCSVRD KVCVKT SPY IEMSCYVAKC NLNTGMCENR LSCDTYSSCG GDSTGSVCKC DSTTGNKCQC NKVKNGNYCN SKNHEICDYT GTTPQCK VS NCTEDLVRDG CLIKRCNETS KTTYWENVDC SNTKIEFAKD DKSETMCKQY YSTTCLNGKC VVQAVGDVSN VGCGYCSM G TDNIITYHDD CNSRKSQCGN FNGKCIKGND NSYSCVFEKD KTSSKSDNDI CAECSSLTCP ADTTYRTYTY DSKTGTCKA TVQPTPACSV CESGKFVEKC

UniProtKB: Galactose/N-acetyl-D-galactosamine lectin heavy subunit 1

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Macromolecule #2: Galactose/N-acetyl-D-galactosamine lectin light subunit 1

MacromoleculeName: Galactose/N-acetyl-D-galactosamine lectin light subunit 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Entamoeba histolytica HM-1:IMSS (eukaryote)
Molecular weightTheoretical: 33.637863 KDa
SequenceString: MIILVLLISY SFGKTQDGKD QLSPNYPYGK MNKDVNFNKP FTSAVDSYQI QQYAENGVFS ANQENYVRAK CKTCCRVIFA SDYNYKTNT QFTDEDDKKG DERYVMDMEF DDKRSVRFRN GGYEQNILLR PLKQGNELQF FEFAPYRMYT SYAIPKRVHD I RGGANEGA ...String:
MIILVLLISY SFGKTQDGKD QLSPNYPYGK MNKDVNFNKP FTSAVDSYQI QQYAENGVFS ANQENYVRAK CKTCCRVIFA SDYNYKTNT QFTDEDDKKG DERYVMDMEF DDKRSVRFRN GGYEQNILLR PLKQGNELQF FEFAPYRMYT SYAIPKRVHD I RGGANEGA TLIIWPKNPP LSDAPGTRNQ RFVYVHPYPT EWYPEYNSTT KYTQNGKTVI KTLKWPTYKR HFYLPYRLDV DL CYQARKA TDGRSTWTGN KNLNTTSKSY QIIASRCSAT EARQIFIPVF A

UniProtKB: Galactose/N-acetyl-D-galactosamine lectin light subunit 1

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60909
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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