9VWJ | pdb_00009vwj

The Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer Rhamnose-binding lectin CSL2 bound with Gb3

PDB DOI: https://doi.org/10.2210/pdb9VWJ/pdb
EM Map EMD-65398: EMDB EMDataResource

Classification: SUGAR BINDING PROTEIN
Organism(s): Oncorhynchus keta
Mutation(s): Yes

Deposited: 2025-07-17 Released: 2026-07-22
Deposition Author(s): Goto, K., Wang, Z., Tsugita, A., Yokoyama, T., Ogawa, T., Tanaka, Y.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9VWJ

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

Literature

The Cryo-EM structure of Chum Salmon (Oncorhynchus keta) 24-mer lectin and Gb3 glycosphingolipid complex reveals a therapeutic potential for Alzheimer's disease

Wang, Z., Goto, K., Tsugita, A., Yokoyama, T., Tanaka, Y., Ogawa, T.

To be published.

Macromolecule Content

Total Structure Weight: 525.99 kDa
Atom Count: 36,504
Modeled Residue Count: 4,680
Deposited Residue Count: 4,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-rhamnose-binding lectin CSL2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	195	Oncorhynchus keta	Mutation(s): 2
UniProt
Find proteins for P86178 (Oncorhynchus keta) Explore P86178 Go to UniProtKB: P86178
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P86178
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], AA [auth a], BA [auth b], CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p], QA [auth q], RA [auth r], SA [auth s], TA [auth t], UA [auth u], VA [auth v], Y, Z	3		N/A	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain QA [auth q] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain TA [auth t] Focus chain UA [auth u] Focus chain VA [auth v] Focus chain Y Focus chain Z

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 1.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	PHENIX	1.21_5207

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	3299
Japan Society for the Promotion of Science (JSPS)	Japan	JPJSBP1 120239904

Revision History (Full details and data files)

Version 1.0: 2026-07-22
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.