Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 127.90 kDa 
• Atom Count: 8543 
• Modelled Residue Count: 959 
• Deposited Residue Count: 1080 
• Unique protein chains: 2

5MR3

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

• PDB DOI: 10.2210/pdb5MR3/pdb

• Classification: CELL ADHESION
• Organism(s): Haliotis rufescens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2016-12-21 Released: 2017-06-14 
• Deposition Author(s): Nishimura, K., Raj, I., Sadat Al-Hosseini, H., De Sanctis, D., Jovine, L.
• Funding Organization(s): Karolinska Institutet, Swedish Research Council, Goran Gustafsson Foundation for Research in Natural Sciences and Medicine, Sven and Ebba-Christina Hagberg foundation, European Molecular Biology Organization, European Union

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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 

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

• PubMed: 28622512 
• DOI: 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.

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Related Citations: 

• 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

• 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

• 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

• 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

• 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

• The crystal structure of lysin, a fertilization protein.
  Shaw, A., McRee, D.E., Vacquier, V.D., Stout, C.D.
  (1993) Science 262: 1864

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Organizational Affiliation: 

Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge, SE-141 83, Sweden. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Egg-lysin	A, C, E, G	136	Haliotis rufescens	Mutation(s): 0
UniProt
Find proteins for P04552 (Haliotis rufescens) Explore P04552  Go to UniProtKB:  P04552

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitelline envelope sperm lysin receptor	B, D, F, H	134	Haliotis rufescens	Mutation(s): 3  Gene Names: VERL
UniProt
Find proteins for Q8WR62 (Haliotis rufescens) Explore Q8WR62  Go to UniProtKB:  Q8WR62

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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	X [auth G], Y [auth G]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	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	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 = 75.87	α = 90
b = 87.86	β = 100.93
c = 92.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-21 
• Released Date: 2017-06-14 
Deposition Author(s): Nishimura, K., Raj, I., Sadat Al-Hosseini, H., De Sanctis, D., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Swedish Research Council	Sweden	2012-5093
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
European Molecular Biology Organization		--
European Union		ERC 260759

Revision History  

• 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