3NK3 | pdb_00003nk3

Crystal structure of full-length sperm receptor ZP3 at 2.6 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.249 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

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

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: https://doi.org/10.1016/j.cell.2010.09.041
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 72.18 kDa 
  • Atom Count: 4,695 
  • Modeled Residue Count: 589 
  • Deposited Residue Count: 654 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zona pellucida 3
A, B
297Gallus gallusMutation(s): 1 
UniProt
Find proteins for P79762 (Gallus gallus)
Explore P79762 
Go to UniProtKB:  P79762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79762
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Zona pellucida 3
C, D
30Gallus gallusMutation(s): 3 
UniProt
Find proteins for P79762 (Gallus gallus)
Explore P79762 
Go to UniProtKB:  P79762
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP79762
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
E
2O-Glycosylation
Glycosylation Resources
GlyTouCan: G00031MO
GlyCosmos: G00031MO
GlyGen: G00031MO

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FLC

Query on FLC



Download:Ideal Coordinates CCD File
F [auth C]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.249 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.385α = 90
b = 98.385β = 90
c = 257.369γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 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
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary