6GF8 | pdb_00006gf8

Molecular basis of egg coat filament cross-linking: structure of the glycosylated 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: 3.10 Å
  • R-Value Free: 
    0.235 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 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: https://doi.org/10.1038/s41467-019-10931-5
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 32.44 kDa 
  • Atom Count: 1,736 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 272 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  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
UniProt
Find proteins for A0A140JXP0 (Gallus gallus)
Explore A0A140JXP0 
Go to UniProtKB:  A0A140JXP0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140JXP0
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.235 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.774α = 90
b = 125.734β = 90
c = 105.001γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.2: 2024-01-17
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-09
    Changes: Structure summary