3D4G

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

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 ...

    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.

    Related Citations: 
    • Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae possessing receptor activity for sperm
      Bleil, J.D., Wassarman, P.M.
      (1980) Cell 20: 873
    • A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor
      Bork, P., Sander, C.
      (1992) FEBS Lett 300: 237
    • The ZP domain is a conserved module for polymerization of extracellular proteins
      Jovine, L., Qi, H., Williams, Z., Litscher, E., Wassarman, P.M.
      (2002) Nat Cell Biol 4: 457
    • A duplicated motif controls assembly of zona pellucida domain proteins
      Jovine, L., Qi, H., Williams, Z., Litscher, E.S., Wassarman, P.M.
      (2004) Proc Natl Acad Sci U S A 101: 5922
    • Zona pellucida domain proteins
      Jovine, L., Darie, C.C., Litscher, E.S., Wassarman, P.M.
      (2005) Annu Rev Biochem 74: 83
    • The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation
      Jovine, L., Janssen, W.G., Litscher, E.S., Wassarman, P.M.
      (2006) BMC Biochem 7: 11
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
A, B, C, D, E
A, B, C, D, E, F, G, H
481Escherichia coli K-12, Mus musculus
This entity is chimeric		Mutation(s): 5 
Gene Names: Zp3, Zp-3, Zpc
UniProt
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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
I, J, K, L, M
I, J, K, L, M, N, O, P
2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth E]
DA [auth E]
EA [auth E]
AA [auth D],
BA [auth D],
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth F],
GA [auth F],
HA [auth F],
IA [auth G],
JA [auth G],
KA [auth G],
LA [auth H],
MA [auth H],
NA [auth H],
Q [auth A],
R [auth A],
S [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
I, J, K, L, M
I, J, K, L, M, N, O, P
alpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.05α = 89.99
b = 91.96β = 90.18
c = 140.48γ = 89.98
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

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View more in-depth experimental data
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: Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Source and taxonomy
  • Version 1.3: 2017-08-23
    Changes: Data collection
  • 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