6GF8

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): 

  • 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: 3.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ab ...

    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: 
    • 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
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden.,Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden. luca.jovine@ki.se.,Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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)
Go to Gene View: ZP1
Go to UniProtKB:  A0A140JXP0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.210 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.774α = 90.00
b = 125.734β = 90.00
c = 105.001γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Cootmodel building
MxCuBEdata collection
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Database references
  • Version 1.2: 2019-07-24
    Type: Data collection, Database references