Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.21 kDa 
• Atom Count: 4727 
• Modelled Residue Count: 581 
• Deposited Residue Count: 654 
• Unique protein chains: 2

3NK4

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

• PDB DOI: 10.2210/pdb3NK4/pdb

• Classification: CELL ADHESION
• Organism(s): Gallus gallus
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


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

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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 

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

• PubMed: 20970175 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida 3	A, B	297	Gallus gallus	Mutation(s): 1  Gene Names: ZP3, ZPC
UniProt
Find proteins for P79762 (Gallus gallus) Explore P79762  Go to UniProtKB:  P79762

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida 3	C, D	30	Gallus gallus	Mutation(s): 3  Gene Names: ZP3, ZPC
UniProt
Find proteins for P79762 (Gallus gallus) Explore P79762  Go to UniProtKB:  P79762

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G	E [auth A]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
FLC	F [auth A], G [auth C]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

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 = 97.7	α = 90
b = 97.7	β = 90
c = 256.419	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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