28YJ | pdb_000028yj

Molecular basis of ZPD homopolymerization: cryo-EM structure of a native vertebrate egg coat filament

• PDB DOI: https://doi.org/10.2210/pdb28YJ/pdb
• EM Map EMD-56971: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2026-03-02 Released: 2026-03-18 
• Deposition Author(s): Banjara, S., Okumura, H., Jovine, L.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network

Fadini, A., Li, M., McCoy, A.J., Banjara, S., Okumura, H., Napier, E., Fontana, P., Khan, A.R., Jovine, L., Terwilliger, T.C., Read, R.J., Hekstra, D.R., AlQuraishi, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 152.48 kDa 
• Atom Count: 6,293 
• Modeled Residue Count: 752 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uromodulin	A, B, C, D	324	Gallus gallus	Mutation(s): 0
UniProt
Find proteins for Q766V2 (Gallus gallus) Explore Q766V2  Go to UniProtKB:  Q766V2
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H, J, K, L	3		N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	I	6		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.60 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	EMReady
MODEL REFINEMENT	REFMAC
MODEL REFINEMENT	Servalcat
MODEL REFINEMENT	PHENIX	2.0_5936

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Banjara, S., Okumura, H., Jovine, L.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2020-04936
Swedish Research Council	Sweden	2024-05336
Knut and Alice Wallenberg Foundation	Sweden	2018.0042

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release