9ENS | pdb_00009ens

Cleavage product of vitellogenin from the honey bee hemolymph

• PDB DOI: https://doi.org/10.2210/pdb9ENS/pdb
• EM Map EMD-19843: EMDB EMDataResource

• Classification: LIPID BINDING PROTEIN
• Organism(s): Apis cerana
• Mutation(s): No 


• Deposited: 2024-03-13 Released: 2025-03-26 
• Deposition Author(s): Montserrat-Canals, M., Schnelle, K., Moeller, A., Cunha, E., Luecke, H.
• Funding Organization(s): Norwegian Research Council, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of native honey bee vitellogenin.

Montserrat-Canals, M., Schnelle, K., Leipart, V., Halskau, O., Amdam, G.V., Moeller, A., Cunha, E.S., Luecke, H.

(2025) Nat Commun 16: 5736-5736

• PubMed: 40593495 
• DOI: https://doi.org/10.1038/s41467-025-58575-y
• Primary Citation Related Structures: 
  9ENR, 9ENS


• PubMed Abstract: 
  

  Vitellogenin (Vg) is the main yolk precursor lipoprotein in almost all egg-laying animals. In addition, along its evolutionary history, Vg has developed a range of new functions in different taxa. In the honey bee, Vg has functions related to immunity, antioxidant protection, social behavior and longevity. However, the molecular mechanisms underlying Vg functionalities are still poorly understood. Here, we report the cryo-EM structure of full-length honey bee Vg, one-step purified directly from hemolymph. The structure provides structural insights into the overall domain architecture, including the lipid binding cavity and the previously uncharacterized von Willebrand factor type D domain. A domain of unknown function has been identified as a C-terminal cystine knot domain based on structural homology. Information about post-translational modifications, cleavage products, metal and lipid binding allow an improved understanding of the mechanisms underlying the range of Vg functionalities. The findings have numerous implications for the structure-function relationship of vitellogenins of other species as well as members of the same protein superfamily, which share the same structural elements.

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Organizational Affiliation: 
• Department of Chemistry, University of Oslo, Oslo, Norway.
Norwegian Centre for Molecular Medicine, University of Oslo, Oslo, Norway.
Department of Biology/Chemistry, Structural Biology section, University of Osnabrück, Osnabrück, Germany.
Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.
Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Aas, Norway.
Department of Biological Sciences, University of Bergen, Bergen, Norway.
School of Life Sciences, Arizona State University, Tempe, AZ, USA.
Proteros biostructures GmbH, Planegg, Germany.
Department of Chemistry, Nova University School of Science and Technology, Lisbon, Portugal. [e-mail].
Department of Biophysics, University of California, Irvine, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 202.22 kDa 
• Atom Count: 9,076 
• Modeled Residue Count: 1,161 
• Deposited Residue Count: 1,770 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitellogenin	A	1,770	Apis cerana	Mutation(s): 0
UniProt
Find proteins for Q868N5 (Apis mellifera) Explore Q868N5  Go to UniProtKB:  Q868N5
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	B	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Montserrat-Canals, M., Schnelle, K., Moeller, A., Cunha, E., Luecke, H.

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Funding Organization	Location	Grant Number
Norwegian Research Council	Norway	262137
Norwegian Research Council	Norway	335244
German Research Foundation (DFG)	Germany	SFB 944
German Research Foundation (DFG)	Germany	SFB 1557
German Research Foundation (DFG)	Germany	INST190/196-1 FUGG

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release
  
• Version 1.1: 2025-07-02
  Changes: Data collection
• Version 1.2: 2025-07-09
  Changes: Data collection, Database references
• Version 1.3: 2025-07-16
  Changes: Data collection, Database references