8RKI

Molecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.331 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.

Nishio, S.Emori, C.Wiseman, B.Fahrenkamp, D.Dioguardi, E.Zamora-Caballero, S.Bokhove, M.Han, L.Stsiapanava, A.Algarra, B.Lu, Y.Kodani, M.Bainbridge, R.E.Komondor, K.M.Carlson, A.E.Landreh, M.de Sanctis, D.Yasumasu, S.Ikawa, M.Jovine, L.

(2024) Cell 187: 1440-1459.e24

  • DOI: https://doi.org/10.1016/j.cell.2024.02.013
  • Primary Citation of Related Structures:  
    8BQU, 8RKE, 8RKF, 8RKG, 8RKH, 8RKI

  • PubMed Abstract: 

    Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.


  • Organizational Affiliation

    Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zona pellucida sperm-binding protein 3320Oryzias latipesMutation(s): 0 
UniProt
Find proteins for Q91184 (Oryzias latipes)
Explore Q91184 
Go to UniProtKB:  Q91184
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ91184
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Choriogenin H170Oryzias latipesMutation(s): 0 
UniProt
Find proteins for P79817 (Oryzias latipes)
Explore P79817 
Go to UniProtKB:  P79817
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79817
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Choriogenin H167Oryzias latipesMutation(s): 0 
UniProt
Find proteins for P79817 (Oryzias latipes)
Explore P79817 
Go to UniProtKB:  P79817
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79817
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.368 
  • R-Value Work: 0.329 
  • R-Value Observed: 0.331 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.35α = 90
b = 108.35β = 90
c = 255.07γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
CNSrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03999
Swedish Research CouncilSweden2020-04936
Knut and Alice Wallenberg FoundationSweden2018.0042

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references