8RKG

Crystal structure of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.cell.2024.02.013
  • Primary Citation of 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XlZPA protein31Xenopus laevisMutation(s): 0 
Gene Names: zp2.Lgp69/64xlZPAzp2ZPA
UniProt
Find proteins for A1L3D9 (Xenopus laevis)
Explore A1L3D9 
Go to UniProtKB:  A1L3D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1L3D9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XlZPA protein188Xenopus laevisMutation(s): 0 
Gene Names: zp2.Lgp69/64xlZPAzp2ZPA
UniProt
Find proteins for A1L3D9 (Xenopus laevis)
Explore A1L3D9 
Go to UniProtKB:  A1L3D9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1L3D9
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseQ [auth I],
R [auth J],
S [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth H],
T [auth A],
U [auth B],
Y [auth D],
Z [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
BCN
Query on BCN

Download Ideal Coordinates CCD File 
W [auth C]BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth G]
DA [auth H]
EA [auth H]
V [auth C]
AA [auth E],
BA [auth G],
DA [auth H],
EA [auth H],
V [auth C],
X [auth O]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.21α = 90
b = 70.31β = 90.037
c = 149.86γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03999
Swedish Research CouncilSweden2020-04936
Knut and Alice Wallenberg FoundationSweden2018.0042

Revision History  (Full details and data files)

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