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- EMDB-65398: The Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer R... -

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Basic information

Entry
Database: EMDB / ID: EMD-65398
TitleThe Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
Map data
Sample
  • Complex: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
    • Protein or peptide: L-rhamnose-binding lectin CSL2
KeywordsLectin / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


rhamnose binding / melibiose binding / cortical granule / galactose binding / protein homodimerization activity
Similarity search - Function
D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / D-galactoside/L-rhamnose binding SUEL lectin domain / D-galactoside/L-rhamnose binding SUEL lectin domain / SUEL-type lectin domain profile.
Similarity search - Domain/homology
L-rhamnose-binding lectin CSL2
Similarity search - Component
Biological speciesOncorhynchus keta (chum salmon)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.89 Å
AuthorsGoto K / Wang Z / Tsugita A / Yokoyama T / Ogawa T / Tanaka Y
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)3299 Japan
Japan Society for the Promotion of Science (JSPS)JPJSBP1 120239904 Japan
CitationJournal: To Be Published
Title: The Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer lectin and Gb3 glycosphingolipid complex reveals a therapeutic potential for Alzheimer's disease
Authors: Wang Z / Goto K / Tsugita A / Yokoyama T / Tanaka Y / Ogawa T
History
DepositionJul 17, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65398.png

Downloads & links

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Map

FileDownload / File: emd_65398.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 360 pix.
= 283.68 Å		0.79 Å/pix.
x 360 pix.
= 283.68 Å		0.79 Å/pix.
x 360 pix.
= 283.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.788 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0308
Minimum - Maximum-0.094349496 - 0.321876
Average (Standard dev.)0.0004318778 (±0.012047424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 283.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65398_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65398_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CS...

EntireName: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
Components
  • Complex: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
    • Protein or peptide: L-rhamnose-binding lectin CSL2

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Supramolecule #1: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CS...

SupramoleculeName: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oncorhynchus keta (chum salmon)

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Macromolecule #1: L-rhamnose-binding lectin CSL2

MacromoleculeName: L-rhamnose-binding lectin CSL2 / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Oncorhynchus keta (chum salmon)
Molecular weightTheoretical: 21.411904 KDa
SequenceString: TRVVTCDNGE NVQFLICDSG VIFIERALYG RTDGTTCKEG RPANQLTNTQ CSQTGTLEVL SHRCNGKQVC EVNTEVFRTS DPCVGIYKY LETTYTCLPA TRSITCEGSD ALLECDEGTI QIHSANYGRR DQLVCSFNRP ANQLANTNCL SQSITTSKVA E RCNRKSQC ...String:
TRVVTCDNGE NVQFLICDSG VIFIERALYG RTDGTTCKEG RPANQLTNTQ CSQTGTLEVL SHRCNGKQVC EVNTEVFRTS DPCVGIYKY LETTYTCLPA TRSITCEGSD ALLECDEGTI QIHSANYGRR DQLVCSFNRP ANQLANTNCL SQSITTSKVA E RCNRKSQC DVPASNSLYG DPCVGTYKYL DVAYTCG

UniProtKB: L-rhamnose-binding lectin CSL2

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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: 6.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9vwi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX (ver. 1.21_5207) / Number images used: 464522
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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