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- PDB-9vwj: The Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer R... -

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Basic information

Entry
Database: PDB / ID: 9vwj
TitleThe Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
ComponentsL-rhamnose-binding lectin CSL2
KeywordsSUGAR BINDING PROTEIN / Lectin
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.89 Å
AuthorsGoto, K. / Wang, Z. / Tsugita, A. / Yokoyama, T. / Ogawa, T. / Tanaka, Y.
Funding support Japan, 2items
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, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-rhamnose-binding lectin CSL2
B: L-rhamnose-binding lectin CSL2
C: L-rhamnose-binding lectin CSL2
D: L-rhamnose-binding lectin CSL2
E: L-rhamnose-binding lectin CSL2
F: L-rhamnose-binding lectin CSL2
G: L-rhamnose-binding lectin CSL2
H: L-rhamnose-binding lectin CSL2
I: L-rhamnose-binding lectin CSL2
J: L-rhamnose-binding lectin CSL2
K: L-rhamnose-binding lectin CSL2
L: L-rhamnose-binding lectin CSL2
M: L-rhamnose-binding lectin CSL2
N: L-rhamnose-binding lectin CSL2
O: L-rhamnose-binding lectin CSL2
P: L-rhamnose-binding lectin CSL2
Q: L-rhamnose-binding lectin CSL2
R: L-rhamnose-binding lectin CSL2
S: L-rhamnose-binding lectin CSL2
T: L-rhamnose-binding lectin CSL2
U: L-rhamnose-binding lectin CSL2
V: L-rhamnose-binding lectin CSL2
W: L-rhamnose-binding lectin CSL2
X: L-rhamnose-binding lectin CSL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)525,99248
Polymers513,88624
Non-polymers12,10724
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
L-rhamnose-binding lectin CSL2


Mass: 21411.904 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Oncorhynchus keta (chum salmon) / References: UniProt: P86178
#2: Polysaccharide...
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 24 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{}}}LINUCSPDB-CARE
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Oncorhynchus keta (chum salmon)
Buffer solutionpH: 6.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21_5207model refinement
13PHENIX1.21_52073D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 464522 / Symmetry type: POINT
RefinementHighest resolution: 1.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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