8RKE | pdb_00008rke

Crystal structure of the complete N-terminal region of human ZP2 (hZP2-N1N2N3)

• PDB DOI: https://doi.org/10.2210/pdb8RKE/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2023-12-25 Released: 2024-03-13 
• Deposition Author(s): Fahrenkamp, D., de Sanctis, D., Jovine, L.
• Funding Organization(s): Swedish Research Council, Knut and Alice Wallenberg Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.

Nishio, S., Emori, C., Wiseman, B., Fahrenkamp, D., Dioguardi, E., Zamora-Caballero, S., Bokhove, M., Han, L., Stsiapanava, A., Algarra, B., Lu, Y., Kodani, M., Bainbridge, R.E., Komondor, K.M., Carlson, A.E., Landreh, M., de Sanctis, D., Yasumasu, S., Ikawa, M., Jovine, L.

(2024) Cell 187: 1440-1459.e24

• PubMed: 38490181 
• DOI: https://doi.org/10.1016/j.cell.2024.02.013
• Primary Citation Related Structures: 
  8BQU, 8RKE, 8RKF, 8RKG, 8RKH, 8RKI


• PubMed Abstract: 
  

  Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.

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Organizational Affiliation: 
• Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden.
ESRF - The European Synchrotron, Grenoble, France.
Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan.
Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan.
Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 115.61 kDa 
• Atom Count: 6,886 
• Modeled Residue Count: 845 
• Deposited Residue Count: 1,005 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zona pellucida sperm-binding protein 2	A, B, C	335	Homo sapiens	Mutation(s): 0  Gene Names: ZP2, ZPA
UniProt & NIH Common Fund Data Resources
Find proteins for Q05996 (Homo sapiens) Explore Q05996  Go to UniProtKB:  Q05996
PHAROS:  Q05996 GTEx:  ENSG00000103310
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q05996-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.68	α = 90
b = 97.77	β = 94.803
c = 104.33	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHARP	phasing
PHENIX	model building
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-13 
Deposition Author(s): Fahrenkamp, D., de Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2016-03999
Swedish Research Council	Sweden	2020-04936
Knut and Alice Wallenberg Foundation	Sweden	2018.0042

Revision History  

• Version 1.0: 2024-03-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Structure summary