Molecular basis of egg coat filament cross-linking: high-resolution structure of the partially deglycosylated ZP1 ZP-N1 domain homodimer

  • Classification: CELL ADHESION
  • Organism(s): Gallus gallus
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2018-04-29 Released: 2019-06-19 
  • Deposition Author(s): Nishimura, K., Jovine, L.
  • Funding Organization(s): Swedish Research Council, European Molecular Biology Organization, European Research Council

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Molecular basis of egg coat cross-linking sheds light on ZP1-associated female infertility.

Nishimura, K.Dioguardi, E.Nishio, S.Villa, A.Han, L.Matsuda, T.Jovine, L.

(2019) Nat Commun 10: 3086-3086

  • DOI: https://doi.org/10.1038/s41467-019-10931-5
  • Primary Citation of Related Structures:  
    6GF6, 6GF7, 6GF8

  • PubMed Abstract: 

    Mammalian fertilisation begins when sperm interacts with the egg zona pellucida (ZP), whose ZP1 subunit is important for fertility by covalently cross-linking ZP filaments into a three-dimensional matrix. Like ZP4, a structurally-related component absent in the mouse, ZP1 is predicted to contain an N-terminal ZP-N domain of unknown function. Here we report a characterisation of ZP1 proteins carrying mutations from infertile patients, which suggests that, in human, filament cross-linking by ZP1 is crucial to form a stable ZP. We map the function of ZP1 to its ZP-N1 domain and determine crystal structures of ZP-N1 homodimers from a chicken homolog of ZP1. These reveal that ZP filament cross-linking is highly plastic and can be modulated by ZP1 fucosylation and, potentially, zinc sparks. Moreover, we show that ZP4 ZP-N1 forms non-covalent homodimers in chicken but not in human. Together, these data identify human ZP1 cross-links as a promising target for non-hormonal contraception.

  • Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1
A, B
136Gallus gallusMutation(s): 2 
Gene Names: ZP1
Find proteins for A0A140JXP0 (Gallus gallus)
Explore A0A140JXP0 
Go to UniProtKB:  A0A140JXP0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140JXP0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.98α = 90
b = 75.98β = 90
c = 101.88γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2012-5093
Swedish Research CouncilSweden2016-03999
European Molecular Biology OrganizationEMBO Young Investigator Programme
European Research CouncilERC 260759

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 1.4: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary