6GF7

Molecular basis of egg coat filament cross-linking: Zn-SAD 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 10.1038/s41467-019-10931-5
  • Primary Citation of Related Structures:  
    6GF6, 6GF8, 6GF7

  • 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 ...

    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.


    Related Citations: 
    • Mouse egg extracellular coat is a matrix of interconnected filaments possessing a structural repeat.
      Greve, J.M., Wassarman, P.M.
      (1985) J Mol Biol 181: 253
    • Abnormal zonae pellucidae in mice lacking ZP1 result in early embryonic loss.
      Rankin, T., Talbot, P., Lee, E., Dean, J.
      (1999) Development 126: 3847
    • Morphological and biochemical changes of isolated chicken egg-envelope during sperm penetration: degradation of the 97-kilodalton glycoprotein is involved in sperm-driven hole formation on the egg-envelope.
      Takeuchi, Y., Cho, R., Iwata, Y., Nishimura, K., Kato, T., Aoki, N., Kitajima, K., Matsuda, T.
      (2001) Biol Reprod 64: 822
    • A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm-egg interaction.
      Okumura, H., Kohno, Y., Iwata, Y., Mori, H., Aoki, N., Sato, C., Kitajima, K., Nadano, D., Matsuda, T.
      (2004) Biochem J 384: 191
    • Mutant ZP1 in familial infertility.
      Huang, H.L., Lv, C., Zhao, Y.C., Li, W., He, X.M., Li, P., Sha, A.G., Tian, X., Papasian, C.J., Deng, H.W., Lu, G.X., Xiao, H.M.
      (2014) N Engl J Med 370: 1220
    • Identification of distinctive interdomain interactions among ZP-N, ZP-C and other domains of zona pellucida glycoproteins underlying association of chicken egg-coat matrix.
      Okumura, H., Sato, T., Sakuma, R., Fukushima, H., Matsuda, T., Ujita, M.
      (2015) FEBS Open Bio 5: 454

    Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden. luca.jovine@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zona pellucida sperm-binding protein 1,Zona pellucida sperm-binding protein 1A, B136Gallus gallusMutation(s): 2 
Gene Names: ZP1
UniProt
Find proteins for A0A140JXP0 (Gallus gallus)
Explore A0A140JXP0 
Go to UniProtKB:  A0A140JXP0
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.41α = 90
b = 75.41β = 90
c = 100.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXmodel building
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