5IIC

Crystal structure of red abalone VERL repeat 3 at 2.9 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 

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: 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: 
    • 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
    • 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
    • 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


    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
Maltose-binding periplasmic protein,Vitelline envelope sperm lysin receptor
A, B
496Haliotis rufescensEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 13 
Gene Names: VERL, malE
Find proteins for Q8WR62 (Haliotis rufescens)
Go to UniProtKB:  Q8WR62
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A, B
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.330α = 90.00
b = 81.640β = 99.60
c = 111.630γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
XDSdata reduction
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-11-29
    Type: Database references