5II8

Orthorhombic crystal structure of red abalone lysin at 0.99 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Egg Coat-Sperm Recognition at Fertilization.

Raj, I.Sadat Al Hosseini, H.Dioguardi, E.Nishimura, K.Han, L.Villa, A.de Sanctis, D.Jovine, L.

(2017) Cell 169: 1315-1326.e17

  • DOI: https://doi.org/10.1016/j.cell.2017.05.033
  • Primary Citation of Related Structures:  
    5II4, 5II5, 5II6, 5II7, 5II8, 5II9, 5IIA, 5IIB, 5IIC, 5MR2, 5MR3

  • PubMed Abstract: 

    Recognition between sperm and the egg surface marks the beginning of life in all sexually reproducing organisms. This fundamental biological event depends on the species-specific interaction between rapidly evolving counterpart molecules on the gametes. We report biochemical, crystallographic, and mutational studies of domain repeats 1-3 of invertebrate egg coat protein VERL and their interaction with cognate sperm protein lysin. VERL repeats fold like the functionally essential N-terminal repeat of mammalian sperm receptor ZP2, whose structure is also described here. Whereas sequence-divergent repeat 1 does not bind lysin, repeat 3 binds it non-species specifically via a high-affinity, largely hydrophobic interface. Due to its intermediate binding affinity, repeat 2 selectively interacts with lysin from the same species. Exposure of a highly positively charged surface of VERL-bound lysin suggests that complex formation both disrupts the organization of egg coat filaments and triggers their electrostatic repulsion, thereby opening a hole for sperm penetration and fusion.


  • Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Egg-lysin138Haliotis rufescensMutation(s): 0 
UniProt
Find proteins for P04552 (Haliotis rufescens)
Explore P04552 
Go to UniProtKB:  P04552
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04552
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
O [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.21α = 90
b = 51.05β = 90
c = 80.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Karolinska InstitutetSweden--
Swedish Research CouncilSweden2012-5093
Goran Gustafsson Foundation for Research in Natural Sciences and MedicineSweden--
Sven and Ebba-Christina Hagberg foundationSweden--
European Molecular Biology Organization--
European UnionERC 260759

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence