5MR3

Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 2.2 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: 10.1016/j.cell.2017.05.033
  • Primary Citation of Related Structures:  

  • 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 gamet ...

    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.

    Related Citations: 
    • 1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding.
      Kresge, N.,Vacquier, V.D.,Stout, C.D.
      (2000) Acta Crystallogr. D Biol. Crystallogr. 56: 34
    • Rapidly evolving zona pellucida domain proteins are a major component of the vitelline envelope of abalone eggs.
      Aagaard, J.E.,Yi, X.,MacCoss, M.J.,Swanson, W.J.
      (2006) Proc. Natl. Acad. Sci. U.S.A. 103: 17302
    • The crystal structure of lysin, a fertilization protein.
      Shaw, A.,McRee, D.E.,Vacquier, V.D.,Stout, C.D.
      (1993) Science 262: 1864
    • The molecular basis of sex: linking yeast to human.
      Swanson, W.J.,Aagaard, J.E.,Vacquier, V.D.,Monne, M.,Sadat Al Hosseini, H.,Jovine, L.
      (2011) Mol. Biol. Evol. 28: 1963
    • Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species.
      Shaw, A.,Fortes, P.A.,Stout, C.D.,Vacquier, V.D.
      (1995) J. Cell Biol. 130: 1117
    • Full-length sequence of VERL, the egg vitelline envelope receptor for abalone sperm lysin.
      Galindo, B.E.,Moy, G.W.,Swanson, W.J.,Vacquier, V.D.
      (2002) Gene 288: 111
    • The abalone egg vitelline envelope receptor for sperm lysin is a giant multivalent molecule.
      Swanson, W.J.,Vacquier, V.D.
      (1997) Proc. Natl. Acad. Sci. U.S.A. 94: 6724

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Egg-lysin
A, C, E, G
136Haliotis rufescensMutation(s): 0 
Find proteins for P04552 (Haliotis rufescens)
Go to UniProtKB:  P04552
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vitelline envelope sperm lysin receptor
B, D, F, H
134Haliotis rufescensMutation(s): 3 
Gene Names: VERL
Find proteins for Q8WR62 (Haliotis rufescens)
Go to UniProtKB:  Q8WR62
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL
Download SDF File 
Download CCD File 
B, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B, C, D, E, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE
Download SDF File 
Download CCD File 
G
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, D, F, H
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.870α = 90.00
b = 87.860β = 100.93
c = 92.550γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
Cootmodel building
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 2.0: 2017-07-26
    Type: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2017-09-06
    Type: Author supporting evidence
  • Version 2.2: 2017-11-22
    Type: Database references