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: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 2.4 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-lysin
A, C, E, G
136Haliotis 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vitelline envelope sperm lysin receptor
B, D, F, H
134Haliotis rufescensMutation(s): 3 
Gene Names: VERL
UniProt
Find proteins for Q8WR62 (Haliotis rufescens)
Explore Q8WR62 
Go to UniProtKB:  Q8WR62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WR62
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth H],
N [auth B],
S [auth D],
W [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
X [auth G],
Y [auth G]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth H]
I [auth A]
J [auth B]
K [auth B]
M [auth B]
AA [auth H],
I [auth A],
J [auth B],
K [auth B],
M [auth B],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
T [auth E],
U [auth E],
Z [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth B],
V [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.87α = 90
b = 87.86β = 100.93
c = 92.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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 2.0: 2017-07-26
    Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.2: 2017-11-22
    Changes: Database references
  • Version 2.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary