ZP-N domain of mammalian sperm receptor ZP3 (crystal form III)

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats

Monne, M.Han, L.Schwend, T.Burendahl, S.Jovine, L.

(2008) Nature 456: 653-657

  • DOI: https://doi.org/10.1038/nature07599
  • Primary Citation of Related Structures:  
    3D4C, 3D4G, 3EF7, 5OSQ

  • PubMed Abstract: 

    Species-specific recognition between the egg extracellular matrix (zona pellucida) and sperm is the first, crucial step of mammalian fertilization. Zona pellucida filament components ZP3 and ZP2 act as sperm receptors, and mice lacking either of the corresponding genes produce oocytes without a zona pellucida and are completely infertile. Like their counterparts in the vitelline envelope of non-mammalian eggs and many other secreted eukaryotic proteins, zona pellucida subunits polymerize using a 'zona pellucida (ZP) domain' module, whose conserved amino-terminal part (ZP-N) was suggested to constitute a domain of its own. No atomic structure has been reported for ZP domain proteins, and there is no structural information on any conserved vertebrate protein that is essential for fertilization and directly involved in egg-sperm binding. Here we describe the 2.3 ångström (A) resolution structure of the ZP-N fragment of mouse primary sperm receptor ZP3. The ZP-N fold defines a new immunoglobulin superfamily subtype with a beta-sheet extension characterized by an E' strand and an invariant tyrosine residue implicated in polymerization. The structure strongly supports the presence of ZP-N repeats within the N-terminal region of ZP2 and other vertebrate zona pellucida/vitelline envelope proteins, with implications for overall egg coat architecture, the post-fertilization block to polyspermy and speciation. Moreover, it provides an important framework for understanding human diseases caused by mutations in ZP domain proteins and developing new methods of non-hormonal contraception.

  • Organizational Affiliation

    Karolinska Institutet, Department of Biosciences and Nutrition, Hälsovägen 7, SE-141 57 Huddinge, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
A, B
481Escherichia coli K-12Mus musculus
This entity is chimeric
Mutation(s): 5 
Gene Names: ZP3ZP-3ZPC
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P10761 (Mus musculus)
Explore P10761 
Go to UniProtKB:  P10761
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP10761P0AEX9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth A]
K [auth A]
E [auth A],
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
T [auth B],
U [auth B]
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.2α = 90
b = 98.58β = 90
c = 143.68γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2021-11-10
    Changes: Database references, Structure summary
  • Version 2.2: 2023-11-01
    Changes: Data collection, Refinement description