3NK4

Crystal structure of full-length sperm receptor ZP3 at 2.0 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report



Literature

Insights into Egg Coat Assembly and Egg-Sperm Interaction from the X-Ray Structure of Full-Length ZP3.

Han, L.Monne, M.Okumura, H.Schwend, T.Cherry, A.L.Flot, D.Matsuda, T.Jovine, L.

(2010) Cell 143: 404-415

  • DOI: 10.1016/j.cell.2010.09.041
  • Primary Citation of Related Structures:  
    3NK3, 3NK4

  • PubMed Abstract: 
  • ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determ ...

    ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.


    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 chicken homologue of zona pellucida protein-3 is synthesized by granulosa cells
      Waclawek, M., Foisner, R., Nimpf, J., Schneider, W.J.
      (1998) Biol Reprod 59: 1230
    • A 42-kDa glycoprotein from chicken egg-envelope, an avian homolog of the ZPC family glycoproteins in mammalian Zona pellucida. Its first identification, cDNA cloning and granulosa cell-specific expression.
      Takeuchi, Y., Nishimura, K., Aoki, N., Adachi, T., Sato, C., Kitajima, K., Matsuda, T.
      (1999) Eur J Biochem 260: 736
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zona pellucida 3A, B297Gallus gallusMutation(s): 1 
Gene Names: ZP3ZPC
Find proteins for P79762 (Gallus gallus)
Explore P79762 
Go to UniProtKB:  P79762
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Zona pellucida 3C, D30Gallus gallusMutation(s): 3 
Gene Names: ZP3ZPC
Find proteins for P79762 (Gallus gallus)
Explore P79762 
Go to UniProtKB:  P79762
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A2G
Query on A2G

Download CCD File 
A
2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
FLC
Query on FLC

Download CCD File 
A, C
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.7α = 90
b = 97.7β = 90
c = 256.419γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-06-18 
  • Released Date: 2010-11-10 
  • Deposition Author(s): Monne, M., Jovine, L.

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-04
    Changes: Database references
  • Version 1.3: 2018-01-24
    Changes: Database references, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary