9E6H | pdb_00009e6h

Cryo-EM structure of Maackia amurensis seed Leukoagglutinin (lectin), MASL


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9E6H

This is version 1.2 of the entry. See complete history

Literature

Maackia amurensis seed lectin structure and sequence comparison with other M. amurensis lectins.

Nayak, A.R.Holdcraft, C.J.Yin, A.C.Nicoletto, R.E.Zhao, C.Zheng, H.Temiakov, D.Goldberg, G.S.

(2025) J Biological Chem 301: 108466-108466

  • DOI: https://doi.org/10.1016/j.jbc.2025.108466
  • Primary Citation Related Structures: 
    9E6H

  • PubMed Abstract: 

    Maackia amurensis lectins, including MASL, MAA, and MAL2, are widely utilized in biochemical and medicinal research. However, the structural and functional differences between these lectins have not been defined. Here, we present a high-resolution cryo-EM structure of MASL revealing that its tetrameric assembly is directed by two intersubunit disulfide bridges. These bridges, formed by C272 residues, are central to the dimer-of-dimers assembly of a MASL tetramer. This cryo-EM structure also identifies residues involved in stabilizing the dimer interface, multiple glycosylation sites, and calcium and manganese atoms in the sugar-binding pockets of MASL. Notably, our analysis reveals that Y250 in the carbohydrate-binding site of MASL adopts a flipped conformation, likely acting as a gatekeeper that obstructs access to non-cognate substrates, a feature that may contribute to MASL's substrate specificity. Sequence analysis suggests that MAA is a truncated version of MASL, while MAL2 represents a homologous isoform. Unlike MASL, neither MAL2 nor MAA contains a cysteine residue required for disulfide bridge formation. Accordingly, analysis of these proteins using reducing and nonreducing SDS-PAGE confirms that the C272 residue in MASL drives intermolecular disulfide bridge formation. These findings provide critical insights into the unique structural features of MASL that distinguish it from other Maackia amurensis lectins, offering a foundation for further exploration of its biological and therapeutic potential.


  • Organizational Affiliation
    • Biochemistry & Molecular Biology Department, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA.

Macromolecule Content 

  • Total Structure Weight: 134.07 kDa 
  • Atom Count: 8,106 
  • Modeled Residue Count: 978 
  • Deposited Residue Count: 1,148 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Seed leukoagglutinin
A, B, C, D
287Maackia amurensisMutation(s): 0 
UniProt
Find proteins for P0DKL3 (Maackia amurensis)
Explore P0DKL3 
Go to UniProtKB:  P0DKL3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DKL3
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, I, K
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, J, L
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
M [auth A]
N [auth A]
Q [auth B]
R [auth B]
U [auth C]
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
BA [auth D],
P [auth A],
T [auth B],
X [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth D],
O [auth A],
S [auth B],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2.5419
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIH GM131832

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-07
    Changes: Data collection, Database references